So it seems that the screen-flip implementation in .3b was immensely buggy; maybe the bottom screen moved to the top, but it happened all the time, and what should be on the bottom screen went missing. It turns out I was using a subtract instead of an XOR to flip. A small thing, makes quite a difference. Flip should work fine now.
Interface issues, and I mentioned that Normmatt had a config editor ready to go. Well, it was still in Visual Basic, and under the GPL, so I ended up only taking a general inspiration from its layout. The editor is available on the new Options menu; try it out.
Download DSemu Here.
Download some DS Homebrew Roms Here, and also some GBA Homebrew Roms Here to try with the emulator.