I tried to draw_rect over the area where I was displaying the score in order to update it too, but that didn't work either. The only way the score isn't a bunch rewritten pixels is when you start a new game. And thanks for the pause loop, I'll try to fix that today.
The score now updates correctly, I had to write a bigger rectangle over the score. Also I'm very interested in running emulators on the 3DS, any chance we can get the source for GB and NES emulators? Do these only run in ARM11?
GB/NES work on ARM9, but very slow, i think if you want dev emulators in bare-metal, you must use ARM11.