I had some free time tonight and pulled the ml_ipod and gen_audioscrobbler projects down from sourceforge. I think I've just about finished with adding support for the newer M4A encoder. Basically, the fourcc for it is different, and so the handling for recognizing valid encoders as well as the logic building the ipod filenames needed to handle that.
Additionally, while I don't know what's wrong with gen_audioscrobbler in its current state, I used some time tonight and converted it to a VS2010 project. For whatever reason, building from that project allows gen_audioscrobbler to show its settings popup without issue, compared to the instant crash with the VS6 build. Obviously this isn't ideal compared to a real fix though, considering it would require everyone to have the VC100 redistributable files to use it. DrO, I know you said at one point you were looking into the actual cause. Did you end up making any progress by chance?
Additionally, it appears that Last.FM doesn't care about out-of-order submissions anymore, so my own build skips some of the spam protection that used to protect the plugin from sending up out of order scrobbles.
A couple snags remain. I can relax gen_audioscrobbler's spam protection, but it still crashes on Vista/7 unless you use the VS2010 build, which is unacceptable for release. Also, the ml_ipod code in CVS is 3.09, not 3.10. I've emailed Abu about this and asked if he could commit 3.10 to source control. After that I'll see about committing the changes. If Abu's busy or not interested, and not able to do a full release (which would totally ok, Abu you rock thank you for working on things as long as you did) then maybe I could at least post a community ml_ipod.dll and gen_audioscrobbler.dll somewhere.