I just updated to NMM 0.40.1, and now when I run Skyrim from it or the SKSE Loader it blanks the check boxes on all of the mods. The only two that it shows as active are skyrim.esm and update.esm nothing else will stay checked, or run. Any ideas or thoughts on why this may be happening? I uninstalled all of the mods, deleted them, and then re-installed them...and it's still doing it.