Try unplugging the power from the dock for 30 seconds and then plug it back in. Then plug the KB and mouse into different USB ports and see if it works. You know the peripherals are fine since they work plugged in directly. When your laptop is docked, check the hardware manager to see if they are disabled while docked.
Do any other USB devices work in the dock? Have you tried a thumb drive? If not then the dock is most likely at fault. If your warranty is still valid I'd call it in.