If you have an XF86Config which doesn't contain the emulthree button options commented, as normally done by mouseconfig / Xconfigurator, but just doesn't have them (or with more whitespace in the comment), then mouseconfig doesn't add these options even if you enable emulatre 3 buttons in the TUI. It would be better todo a wildcardsearch for these options and remove any lines containing them and then just blindly add them again (commented or not depending on the users choice), this will also work with custom XF86Config files, like mine.
trond, please see if you can fix this.
The XFree 3 parser tries to be clever and preserver options:( - I would rather have them running Xconfigurator... the alternative is rewriting that part of the code to do like the XFree 4 version: Don't care about what is in the existing file, just write the current values.