Good news, I figured out why some files aren't syncing to handhelds. I've been having this problem ever since 290 as discussed
http://yabb.jriver.com/interact/index.php?topic=28252.0.
The problem is, if the Name or Album (or maybe Artist too) has a character in it which is not valid for a path, then it can't copy the file to the handheld. This appears to only happen when the file is re-encoded. I don't know why it works ok if it is just copied.
Here's an example:
I have Meat Loaf's "Bat out of Hell II: Back Into Hell" album. I originally ripped this with WMP before I started using MC. WMP converted the ":" character a "-" character for the path in which the file was placed, but the Album tag still uses the ":" character. When I try to sync any of the tracks in this album MC converts the file file, but then fails to copy it to my handheld. If I rename the Album to use a "-" instead of a ":" then it works fine.
I don't think the fact that I originally ripped in WMP matters, though.