That's very interesting. No issues here on 3.1.3 jailbroken iPhone original, 4.3.3 jailbroken iPod Touch 3g, or my friends 4.3.1 jailbreak on his iPhone 3GS.
Generally, jailbreaking all by itself doesn't cause bugs that would interfere with a sandboxed application. Try booting into Safe Mode - the fact that you know you have no MobileSubstrate hacks installed probably means you have MobileSubstrate installed and are not 100% sure what's going on. If you do not know how to boot into safe mode, go into Cydia, install SBSettings, respring, slide the top bar of your iDevice, press power and then Safe Mode. Once you have done so, try playing the game again. If that didn't work then restore and unjailbreak.