I can confirm that the message in small tiny box windows saying fail to initialise.... "to render" (cant seee due to window so small ), game fail to load... is definitely caused by mod manager. Mod manager installs "mo1.dll" and mo_ path.txt to the \data\skse\plugins\ folders - Simply remove these or mainly the mo1.dll and the message goes away.
Althoug it not ncessary as skse wil run with or without it. It simply so that mod manager can run the skse app within its gui.
Apoligies just tested again - even by leaving the mo1.dll skse still loads without the error. The error is infact caused by the mo_path.txt (This the contents of my mo_path.txt :- D:\TEST\ModOrganizer) so simply the mo1.dll is looking for mod organise installtion or source directory where want to load from but cannot as it s been removed its location or the disk.
PS I removed mod organise about two days ago and the message was irratating me! lol
Zyp from Nexus
(Real Life IT Technical Support Specialist - Ex-Programmer)