I am having that issue as well with the 996 and 396 for some reason, i am trying to narrow it down but there was a post on the ARC396 yahoo group, did not see a resolution to it yet though, but it is very annoying after working on large systems and then i have to go back in and cut and paste the frequencies back in, seems to happen after quick saves and writes to the radio
this does not neccessarily occur when you close the system file though