Ok, I think we've all concluded gpsp isn't working right.
No developer is looking into this issue, at this moment.
To be able to solve it, you'll need some specialized knowledge about the GBA, gpsp, and probably the 3DS itself.
Maybe try to discuss a possible solution?
A few possibilities are:
- Learn C and try to fix it yourself.
- Wait until someone else learned C and fixes it for you.
- Start a bounty to get someone, who does have the skill and interest, to fix it for you.
O, and last but not least..
- forget about gpsp and hope mgba will reach the level you wish (and gets included in retroarch again).