It's hard to know what any compatibility issue may be since you don't tell us what brand of dock/charging station you bought.
One thing I can say for sure is that the 3rd gen iPod doesn't charge via a usb connection only via firewire, so that is most likely the reason the iPod is not charging.
Almost certainly, the dock/speaker system you bought will not be connecting to the pins on the iPod's dock connector that charge it.