Well, then I am not sure what the problem is.
All I could suggest is re-copying the game file back over or re-downloading it. But Since you have tried with multiple consoles, I think you may have already had that idea.
Unfortunately, Doom for GBA lags really, bad and the SNES version doesn't even work for me. So you can't even have a proper substitute. Doom 2 for GBA works pretty ok though for some reason.
Sorry I couldn't be more help.
Maybe you could try reinstalling the firmware?