Okay, after some playing around, I learned a few things.
1) For some reason, only the 32-bit version of this emulator is detecting those codecs. The 64-bit version isn't detecting them at all.
2) Only FFDShow is recording properly. When I try using x264, it desyncs.
3) When I try to record higher than 32kHz, the emulator crashes.

(EDIT: I found that if I switch the audio source to SNES9X DirectSound, it doesn't crash.)