I'm not sure. But this Game has a copy protection.
At one specific position in game you can't play any longer if it runs on an emulator, or you play with a copied disc.
Copied from
http://db.gamefaqs.com/portable/gbadvance/file/rockman_exe_a.txt
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Important Note to Emulation Users:
"It's common theft, man! Nothin' more, Nothin' less!" - Grit
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Rockman.exe features extremely clever copy protection. Using a key
from old Amiga/PC games, they've rigged it so that when a ROM image is
dumped, it becomes impossible to open the final door before Number Man.
In other words, it's impossible to beat the second area playing on a
ROM, don't even waste your time.
That said, WHAT THE HELL ARE YOU DOING TRYING TO EMULATE A GAME
THAT CAN STILL BE BOUGHT?!? EMULATION IS FOR RETROGAMING DAMNIT! IT'S
COMMON THEFT TO EMULATE GAMES YOU CAN STILL BUY! I OWN THE CART, YOU
SHOULD TOO!
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