I recently contacted the author of mod organizer about this specific problem, and he stated that the current stable version 12.9 is not working properly in the save profile section.
He recommended me to try the new beta version 0.99.6 which seems to have fixed all of the problems from the previous version. (including the save profile bug)
So anyone having similar problems like myself, install the new beta version and see your problem disappear.
Moderators, you may close this topic as solved. Thanks
