Is your ipod dock certified for the use with your ipod? Charging and transferring data between the devices are using different contacts in the docking port.
More info here: Troubleshooting iPhone, iPad, and iPod touch accessories
The ipod shuffle uses other contacts than the ipod touch inside the docking connector. So if your ipod dock is not made to work with the ipod touch, it can't.
My Bose dock 1G, for example, was not made for the use with my iphone 4, as a result, I can play music from my iphone, but the dock will not charge it, although my ipod and my iphone 3G do both things, play music and getting charged, mo problems with my old Shuffle either.