This doesn't sound like a problem with your patch. There is no limit to the amount that you can change as long as you're doing it correctly. Even so, patching an ISO shouldn't mess with your controls like that. If I had to guess, I'd say it's your emulator. Have yo updated anything on your computer since you installed the emulator? That's most likely the cause of something like this. Like Kadwin said though, try with the simple first. Try patching a clean ISO. If nothing works, why not give a system restore a go?