I noticed this happened to me, but then it stopped... it may just because I zoned, or camped to another character after closing it. I think I closed it, re-opened it, closed it, zoned, camped to another character...
Hmm, sounds like a different but similar problem. I guess I was pretty sloppy when adding my hooks to save the window because I missed a save when it opens and closes and must have missed a save when you move it.
Try putting it where you want, then using the /save_uisettings command to force a save.