I'm curious as to why so many people encode mono tracks to joint stereo. Is there a quality hit involved in encoding single channel that I'm unaware of?

On the same issue I encode numerous single channel tracks using alt-extreme and get a lot of 256 and 320 frames. As these are single channel my logic says that these correspond to 640 kbs stereo frames. Does this have a problem in any compatibility. They play fine on all of my hardware players.

AFAIK: MP3 format allows frames to have up to 320kbps size (width?) for either MONO, JOINT STEREO, DUAL MONO and LR (simple) STEREO - so this is not an error. You may find it appropriate to strip the file to one channel (left or right - whichever You may find recorded better) and encode as something like --alt-preset extreme -b 96 (I've seen similar suggestions to encoding MONO (or single channel) files using --alt-preset standard. Hope it in some way helps You