Looks like we have stepped through all the games that I have found have problems except:
Satan's Hallow - seems to have issues with the keyboard.
Dave's Midnight Magic - same issues as Satan's Hallow
My guess is they did some illegal calls to the keyboard controllers that the other emulators caught. So, maybe an update will fix?
Now I haven't tested every homebrew, one off or much of the development and other apps. So if you come across another program that won't work just post here as someone my have a working version.