I too noticed my ESPs getting unchecked. Its been reported in the Issue Tracker here: https://issue.tannin.eu/tbg/modorganizer/issues/1160 "confirmed. right now the MO switches to the top-most profile immediately after closing the profile management dialog and then switches back to the one that was selected before." I was able to replicate exactly that. I also noticed that MO saves the profile even if its not dirty (i.e.: hasn't been edited) so be careful I found it easy enough to re-enable them by using the "Fix Mods" feature in the "Saves" tab (MO is ****ing amazing!).