Are all these windows from the same file or do you have windows from more than one file here?
I have seen cases where windows to other filemaker files disappear from the window menu. I can usually find them (on my windows xp platform) by either minimizing all the other windows or by by selecting the file from File | Open recent.
To avoid such window issues and make things simpler for my users, I always put navigation buttons on each layout for the user to use to move from window to window and file to file. I've also added a custom menu to the standard list of filemaker menus for this purpose.
Using FMP11.0v3 I'm having a similar problem, but I cannot find any use of AdjustWindow[hide] in our database's scripts. We do have several points where the window gets maximized by a script. Our database was created years ago in older versions of FM and has many tables spread across multiple related files.
I posted some more info in this thread: http://forums.filemaker.com/posts/144ce11623