Alright, well I don't know why but its working now (thru MO) and the CK sees all the plugins.
What I did: Unchecked the "run as administrator" for both MO and CK executables. Unchecked compatability mode for the CK.exe (I had set it to Win 7 --I'm running Win7 Ult 64bit) Moved (edit: a copy of) the plugins.txt from my currently loaded profile to the F:Steam...Skyrim installation folder This removed the elevation prompt when launching the CK from MO however the CK failed to launch and MO hung at the "MO is locked while running the executable" msg.
Then I cut the plugins.txt that I had pasted into the F:Steam...Skyrim folder and pasted it to desktop. Now the CK launches fine and sees everything installed for my current profile. I'm at a loss as to why its working though.