If certain windows don't seem to be saving their positions but others are, then I suspect a messed up UI settings file. Sometime ago I had a few bags that would never remember their location. As it turned out I hit some limit on the number of XML entries for bags. It still had settings for small bags that I had quit using a long time ago.
Anyway, look in the EverQuest directory for a file that looks like (server-name)_(toon-name)_eq2_uisettings.xml and rename it or back it up somewhere and delete it. When you go back in the game it will put everything back at default positions/sizes and recreate the file.
Now, see if you can move the problematic windows and save their positions.
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