i think you should start to watch a bit closer to what you do before this apparently happens. i'm pretty certain that things do not just save themselves just like this. we're not seeing those things here.
note, when you start Rig Manager it will sync the content of your Profiler. So, assuming that things change over night the pretty much only chance for this to happen is that those changes you did never made it to your Profiler. And this could well have to do with an issue related to the connection. I'm just thinking out loud here.
With all due respect, I think I'd know if I saved it manually - and there were no changes made to the profiler that would have needed to be reflected in RM. It is also not 'apparently' happening, it IS happening. As stated, I did not save anything either via RM or the Kemper before this happened; this occured directly after the upgrade procedure.
The upgrade workflow for me was:
1. Turn on Kemper
2. Load RM
3. Update via RM
I'm just going to downgrade and wait for the release, as the latest beta's have been far too buggy IMO.