Damn it. That's always the problem, lol. Switch between 64k and 128k and then see if it works (ie, try it on 64k, and failing that, switch back to 128k and try again. Surprisingly it sometimes works, even if it hadn't before). If that doesn't work, try the Frequently Asked Questions thread in Emulation and see if it's there, (or one of the Stickies, they usually have the information for starting up Roms, etc).
I have a serious problem on VisualBoy Advance (emulator), when i boot up Pokémon Emerald (aka. the game with animations), the screen turns white and it says "Loaded Battery" and no more, just white.
Just for future knowledge, never post Emulation-related questions in any other section other than the Emulation section. It's frowned upon, big time. Basically, Rom's are illegal (basically), and so the staff kinda want to keep Emulation stuff contained to one section, I guess.
To solve your problem, I think it's something about the Save Type. In VBA, go to options/settings, and Emulator (I think they're called that, sorry). Anyways, find a sub menu labelled Save Type, and select Flash and Flash 128k. That should fix the problem.
This wasn't telling you off or anything, just trying to help you avoid any trouble.