Are you sure that you have appropriate video modes installed for those emulators/games?
GM simply chooses the best mode from what's available, so will usually just "work", but other emulators typically use specific modes and if you don't have them, won't work right (Disclaimer: I say that generically, I don't actually use the emulators you mentioned other than GM).
Check your help, ini and log files, if available, to see what video modes your emulators are looking for.