What program should I use to manage an iPod Shuffle (4G)?
You might want to try Floola. I haven't tried it on a shuffle, but I've had good success with a few different iPod models with it:
http://www.floola.com/home/
Try Banshee once more and update it if not latest, which can sync ipods of many types . I've tried it myself with a mini Try Pearlpod as an alternative