Hang on a second here. I have a similiar issue running the same version of software. We added user rights to an IP Office, applied to a set of users and merged the config. I was able to tell that the changes were accepted because the buttons were setup on the users phones. When we went to reopen the configuration there was no user rights group, but the Users we were testing with still showed the user rights group assigned in Manager under their user profile, no buttons on thier button programming tab, but the buttons were still working on the phone.
I think it's definitly strange. No errors writing to the SD card and only one instance of Manager was open.
Any thoughts here, buggy software? Have you been able to get your Hunt Groups to re-appear or did you manually add them back in again...
This is making me wander what else is missing?