When you upgraded did you by chance change the user account that the ipMontor service is running under? It sounds like the service account may not have write permissions to the ipMonitor\config folder so the changes don't get written to disk on service shutdown...You can go into the ipMonitor config application to view/change the account.
Hope this helps!
Its not the permissions. Changes to the objects and monitors do take.
My suspicion is that it has something to do with upgrade process. Some of these monitors are really old and were created back in the day with ipmon v7.x
What I did to remedy this problem was to recreate the devices and monitors.