Absolutely. Games sometimes have weird issues when defaults are changed, even on released code. Ripley's had an issue where if you set Asia to require more than 30 switch hits, it would reset. And that was on later code. It was fixed, but the bug was introduced when the code was almost done. Proto ROMs should always be considered suspect.

If you think a setting borked your game, unplug it, pull the batteries, wait half an hour, then try again.