I too have an iPod Shuffle 4th gen that would not sync with MM4. My symptoms were that some tracks would be skipped during sync in MM4, tracks would be sent to the Shuffle but would be skipped by the Shuffle during playback, or tracks would not be recognized at all by the Shuffle and I would receive the message to "use iTunes to add tracks".
I have found a work around.
1. Plug the iPod Shuffle into the USB port on the computer.
2. Start MediaMonkey.
3. Use MediaMonkey to add music to iPod Shuffle, or to remove music from iPod Shuffle.
4. Leave the iPod Shuffle connected to the computer (do not click Safely Remove, and do not unplug the iPod Shuffle from the USB port).
5. Close MediaMonkey.
6. Start iTunes.
7. In iTunes, click iPod Shuffle.
8. Click Music, and then verify that the music you want is on the iPod Shuffle.
9. Click the arrow next to iPod Shuffle to disconnect the iPod .
10. Listen to the iPod until you want to change the songs again.
11. Repeat these steps.