I don't know if you already solved it, but I had the same problem yesterday. The problem is in the rom size.
I was trying to get a brazilian translation of Golden Sun running on the app, the game opened, but I'd get a black screen.
In the end the problem was that the rom had like 8,56MB, which the GBA app can't read as a 8MB rom nor a 16MB rom. I don't know why some games with different rom sizes worked, but in Golden Sun's case, I had to use HackRomTools - XSE to expand the rom size to 16MB. After doing that, the game ran flawlessly.
The same thing happened with an english translation of Crayon Shin-Chan, the game only booted after I expand the rom size!