Windows not remembering their locations may be an issue with your uisettings.ini file, at least for my UI that was one of the reasons with the disappearing bottom bar.
Except for bags occasionally moving around when switching resolutions I do not think I ever had something move off screen, though. My examine windows always stay put.
If you continue to have issues with windows getting lost, however, and it is not your uisettings.ini, you can probably just add an OnShow code to the first line (the page tag) of your windows to repositions them when they get openend, e.g. OnShow="Location=0,0" to put them in the upper left corner.
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