Update:
I did a little digging and found out that yGather stores the resource database on the 'savevariables'. I got a little suspicious and uninstalled the mod and the random resetting of 'savevariables' seems to have disappeared.
Don't quote me on this, but my theory is that when you play and yGather gathers info about resource locations and when you exit the game and the data is saved. If the yGather data is big enough the file write could maybe fail before all the data has been succesfully saved, which means corrupted file -> RoM client creates a new, clean file. Or the file gets too big to read and it fails at that point
I dunno, I need more time to see if the problem is really gone, but I suggest that if you have yGather installed and this problem occurs, try disabling the mod and see if it helps.