For enboost I followed STEP's guide, which differs from the nexus mod version and never had any issue:
http://wiki.step-project.com/ENBoost
You will also want to enable the memory tweak for skse (now my preference) or install smse.
http://wiki.step-project.com/Skyrim_Memory_Patch_3.0
The OP probably covers this off anyway, but if you follow the STEP links provided you should not have issue. Assuming this is the cause of your problems and not the installation and removal of mods on a current save file you alluded to before.
Hope that helps.
http://wiki.step-project.com/ENBoost
You will also want to enable the memory tweak for skse (now my preference) or install smse.
http://wiki.step-project.com/Skyrim_Memory_Patch_3.0
The OP probably covers this off anyway, but if you follow the STEP links provided you should not have issue. Assuming this is the cause of your problems and not the installation and removal of mods on a current save file you alluded to before.
Hope that helps.