GSDFan

This is normal behavior for MO2. MO2 strives to keep the games folder and data folder clean from the mods installed and activated in the left mods pane. When an executable is run from within MO2 it uses its virtual file system, VFS, to present those files to the game. 
Yes this is true.
 
Settings / paths.

Your "Base Directory" is the home location of your instance. Depending on how you did your install it may contain the Downloads, Mods, Caches, Profiles and the Overwrite mod, and yes it is a folder but MO2 refers to it as a mod. It can also contain the MO2 related files.
Use the folder icon on the toolbar to access all of your folders.

I was doing some reading of issues on the Mod Organizer github and stumbled onto an issue the same as yours, crashing when launching applications through MO2. A couple of users there stated there they were using BitDefender Antivirus. They also stated that they were also using BitDefenders Advanced Threat Defense which is separate from the AV.
It looks like one of the users outright disabled the threat defense and the other made some exceptions to the advanced threat defense.
I took the liberty to copy them here in case you also use that.
(MO2 Install Directory)\modorganizer.exe (MO2 Install Directory)\ufvfsZ_Zproxy_x64.ext (Skyrim special edition Install Directory)\skse64_loader.exe (Skyrim special edition Install Directory)\skyrimse.exe  
From <https://github.com/ModOrganizer2/modorganizer/issues/1808>

Edit, press the left Pane Backup button first and then do the below.
Go to settings, Workarounds tab and on the bottom left press the :Reset Window Geometries" button. A dialog will pop up select the restart Mod Organizer to reset. MO will restart with default size.
If the mods in the left pane are sorted alphabetical order, then restore the backup.

While I don't know the exact cause of this, I traced it down to my Smashed Patch. I was trying out the smash.all setting and kind of forgot about that. I guess it is back to a custom built smash setting.
 
Thanks

The Mod "Oblivion Camera SE" is a Skyrim Script Extender Special Edition, SKSE, Mod. As the mod does not contain an ESM, ESP or ESL there is not going to be a "Blue Bar" in the scroll bar areas right pane. It will only show up when there is one of the previously mentioned file types and the mod is selected in the left pane.

Not that I am aware of.
Sounds like a pathing issue or corrupt  ModOrganizer.ini. The quickest way to test is to reset is to shut down Mod Organizer and rename ModOrganizer.ini to something else. This will in effect simulate a clean install. Your tools will need to be setup again and your mods may be gone also from the interface, but do not panic they are still there. Run the game once from the launcher to establish registry values and shut down the game. Start MO and test. MO should grab what it needs and you can point it to your downloads and mods folders from the path settings if needed. Don't touch any other paths in the settings.

Not that I am aware of.
Sounds like a pathing issue or corrupt  ModOrganizer.ini. The quickest way to test is to reset is to shut down Mod Organizer and rename ModOrganizer.ini to something else. This will in effect simulate a clean install. Your tools will need to be setup again and your mods may be gone also from the interface, but do not panic they are still there. Run the game once from the launcher to establish registry values and shut down the game. Start MO and test. MO should grab what it needs and you can point it to your downloads and mods folders from the path settings if needed. Don't touch any other paths in the settings.

From each of the install folders of MO for the games you have, start MO.
Press the top most left icon, the gray over the red arrow, to start the instance selection process.
Press OK at the are you sure dialog. A new window will show with Oblivion at the top followed by New, Portable and Manage.
Press portable and it will restart. You should get a new window with the installed games, select the game needed for the folder. MO should restart with the game chosen.
Go into the settings and check that the base directory points to that folder.

Not a problem and thank you fro reporting back.

Not a problem and thank you fro reporting back.

You have to make a new shortcut to Tes5Edit and specify "-quickclean" as an argument. This will run the program in the cleaning mode for a selected mod.

If you do not have the OBSELoader in the games directory the option for the Script extender will not show up. If you have the GOG version of Oblivion then you need the OBSE GOG version. My MO2 did not show the Script extender option until I installed the GOG OBSE loader and restarted MO. MO has to see the loader and when it does, it will show in the executables and the script extender work around.

At the bottom center of the left pane you have the drop down of the grouping option set to Nexus IDs. Set it to no groups to get rid of that.

You may have tried to install the file before it fully downloaded or it may be corrupt. If you downloaded it with the "download with manager" button then try to download it through your browser and see what happens.

You have the left pane sorted by categories or nexus IDs. Click the drop down box in the center bottom and select No Groups.

Feature requests are better made on the Github Issue Tracker and will be seen by Tannin there before here.

Feature requests are better made on the Github Issue Tracker and will be seen by Tannin there before here.

Shut down MO and use Windows file explorer to go into the  ModOrganizer\webcache folder and delete the files and folders there. Restart MO and you should now be able to log in with the new info.

Yes you can.
 
Assuming that the left pane is sorted by priority and zero is at the top, which it looks like it is. Then as the picture shows Skyrim HD- 2kTextyres would have a higher priority that Serious HD Retexture. If you were to reverse them then Serious HD Retexture would win any conflicts.
 
Remember this is for any files that conflict between mods. If there aren't any conflicts then it is not a problem.

Clear out the login info in the nexus tab and OK out to the main interface. Close MO and go to the MO install folder and look for the webcache folder. It should be ModOrganizer\webcache. Delete the files and folders in there. Restart MO and you should not be logged in anymore.

Double click the mod and select the "Nexus Info" tab, Mod id is on the top left. You can change the mod is and Version there.

The proper way to use MO, Oblivion and OBSE is to set the “Launch Mechanism†in the workarounds tab to Script extender and Launch the game from Steam. This means that you mod in MO and run the game from Steam. You also need to enable the Steam community in game option in Steams Oblivion settings.
 
If you try to run the game from the MO configured “OBSE†shortcut you will get the “You are trying to use a Steam version of Oblivion. Steam users should launch the game through Steam, not by running obse_loader.exe. If OBSE fails to load, go to Steam > Settings > In Game and check the box marked "Enable Steam community in game". Please see the instructions in obse_readme.txt for more information.†message and the loader will exit.
 
If you run the shortcut “Oblivion launcher†the launcher will open as usual. If play is pressed it will close and open again and when play is pressed the game will start.
 
If the MO configured shortcut “Oblivion†is run the configuration utility will open up and you can run the game from here.
 
In all of the above situations you should not be running the game from here. Steam needs to be the mechanism to do this.
 
My theory on this, whether right or wrong, is that Steam launches the game, then the "in game community" which in turn allows obse_1_2_416.dll and obse_steam_loader.dll to do their work. The file obse_loader.exe is not needed for the Steam version of the game. It is for the retail version of the game only and should be deleted.
 
Running the game from Steam will allow the launcher to run first. At this point MO has not been loaded and if you view the Data files only the vanilla game directory will be seen. The launcher is reading the Oblivion.ini in the "My Games" folder and DLCList.txt and Plugins.txt from C:\Users\username\AppData\Local\Oblivion folder. Any changes made here will be written to those files and not the ones in the active MO profile.
 
Pressing the play button will allow the game to start, which in turn launches the 'in game community" and then allow the OBSE_XXXX.dlls to load, which will load MO as a script extender from the games vanilla directory. MO should now be active and the VFS and all of the MO mods should be loaded.
 
 

I am marking this solved with the solution below, I can't mark the OP as solved.
 
SOLVED:  With the help from RoyBaatterian over on his nexus mod pags for Fallout |New Vegas 4GB Updated, this problem I was having has now been solved.  It turns out that it was a problem with my video driver not correctly detecting the game, due to the different file name.  I was instructed to download NVIDIA Inspector so I could add a profile for the FalloutMO.exe.  

After spending many hours trying to solve this, it turns out there was a simple solution.  Thanks again to Roy and everyone else who tried helping me with this.

This will happen when a setting in MO get unchecked. Press the wrench and screwdriver icon to open the settings window. Select the Workarounds tab and make sure the Force-enable game files is checked. press OK to exit and either refresh from the drop down menu next to the profile selector or restart MO.

It is basically two part install.
 
In the main blocksteal redux 1_4_1 untick the PreventsAccidentPickup.bsl and the text files. There is already a SKSE folder in the archive. Make note of the name of the mod. Click OK to finish.
 
The second file to install is “All vannila miscItem basket text by White Shadow†with file “PreventsAccidentPickUp.basket†in it. That archive is not properly set up. On install make sure the filename is the same as that first part. Click on the “<data>†right click and select create directory. Name this directory SKSE. Click on the SKSE, right click and create a new directory called Plugins. You will now have SKSE\Plugins. You can now drag the PreventAccidentPickUp.basket into the Plugins folder.
 
If you did everything properly MO will ask if you want to merge or replace the mod, select merge.
 
 
 
This is the SKSE\Plugins directory

 
This is the second file to install

 
This is the merge dialog