Removing that file doesn't seem to help, though. Let me see if I can make it clear what happens, for those who don't know anything about wine:
When I install a Windows program using wine, it is installed to "/home/xxxxme/.wine/drive_c/Program Files" (by default, Geneforge 5 would be installed in "/home/xxxxme/.wine/drive_c/Program Files/Spiderweb Software/Geneforge 5").
The "registry" is in the files "/home/xxxxme/.wine/*.reg".
wine puts things for "My Documents" in "/home/xxxxme/.wine/drive_c/Documents" (this is custom).
I've deleted the whole Spiderweb Software directory (I hadn't any saved games yet) from "My Documents", yet Geneforge 5 still doesn't ask me what resolution to use when I start it.
When I rename my "/home/xxxxme/.wine" directory, make a new one, and install Geneforge 5 there (like installing it again after reinstalling Windows, if I were using Windows), I -am- asked what resolution to use when I start it.
The problem with just using a new .wine directory for Geneforge 5, though, is that I have other things installed with wine, in the old directory, that I want to keep, and don't really want to reinstall all of them.