Ok I tested this a couple of times now. This is my procedure.
1. In iTunes restore the ipod to make sure it is as clean as the factory
2. Tell itunes NOT to launch when ipod connected.
3. Sync iPod with MC
My music is FLAC formated and I convert it to mp3.
On top of the fact that over half of my cover art images are not loaded on the ipod (think this is already being worked on), I get stuttering during playback. This does not happen if I load the same music with iTunes. By same I mean the same converted mp3s that MC creates.
I also noticed that the stutter is more frequent if I load a larger library.
When searching for a cause to this I came across this page.
http://yuo.be/wiki/dop:dopI added lots of artwork to my iPod and now my iPod stutters when playing music
This seems to be caused by fragmentation of the artwork .ithmb files. You can defragment your iPod to resolve this, but do not leave the defragmentation process running for an extended period of time as this will put undue stress on your iPod. Note: Apple does not recommend defragmenting your iPod. In the future, using the latest version of foo_dop and sending several files to your iPod in a single pass (i.e. not a single or few files at a time) will help avoid heavy fragmentation of the .ithmb files.
I am wondering if the way MC is loading the coverart is causing excess fragmentation. The stutter also is not reproducible in the same location of the music file which tells me the issue is during playback and not with the mp3 file.