Some mouse-only games are still setup to use just controllers and not the attached mouse/keyboard when you use the WHDLoad version. Populous, for example. I don't know what i need to do to unset that, so I can't make any suggestion for you on this either (if it's the case).
My only other suggestion would be to disconnect your controllers before firing up an amiga game and/or switch USB ports so that your mouse and keyboard are on the lower port numbers (0 and 1).