I'm new to the board, but already a big fan of the Monkey. Perhaps this issue is new:
Using Media Monkey beta build 1493, IPHONE 4 with iOS 5.1.1 and ITouch 4 with iOS 5.1.1.
Syncing the IPHONE is a snap, no issues synching via a Playlist or with an individual song. The ITOUCH is a different matter. It seems to use the same plug in, and a single song from the Monkey library appears to sync just fine, but it isn't there. The internal directory on either "device" is the same - /ITUNES_Control/Music....
Once a sync for a single song is complete, it just isn't there on the ITouch. Media Monkey can't play it directly, although when browsing the device after sync, it shows that it is there. Unplug the ITouch and plug it back in to browse again, the song is not there.