I've deleted my INI files, set everything up from scratch, and still have the same issue. (Bags not staying put)
One thing that I noticed is that the position of some windows seems to be getting set relative to the letterbox, and others to the screen border. I changed the size of the letterbox and 2 of my bags moved with it?! Is there something in the xml I should be looking for to tell it to use absolute positioning for all of the bag windows? I currently have no letterbox which I thought might help, but my bags still come back to the same goofy spots whenever I log in.