First, Rhythmbox on Ubuntu 10.04 wouldn't recognize the SD card. Fortunately, I'd stumbled across the solution to that a few weeks ago: put a file called ".is_audio_player" in the root of the SD card.
However, it still wouldn't copy m4a files over. The DS only plays m4a files, not mp3. I discovered that you can actually put content in the .is_audio_player file to control the behaviour of Rhythmbox. It was still hard to figure out what to put in, but finally I looked up what Rhythmbox uses to manage an iPod, and put this in the .is_audio_player file:
Worked a charm after that.
P.S. My son's doing some serious scratch with the Police on his DS right now.