I'll explain things via some screenshots.
http://imgur.com/mUPkmoy <- clearly selected as AVI
http://imgur.com/LGL2cmC <- record microphone in separate track
http://imgur.com/qYnt98h <- mp4 file
http://imgur.com/4DbzPlZ <- yep it's an mp4 file
http://imgur.com/vxSC4mC <- one audio track
This is INFURIATING. No combination of settings will get my videos to have my mic as a separate audio track NOR can I get the damn thing to record in avi (because, despite having done it in the past, I've read that nVidia MP4 can't do separate audio tracks??).
Seriously, what the heck. This is ridiculous. It's like the program arbitrarily decided it doesn't like my settings.