What model shuffle is it? This document shows the four types.
http://support.apple.com/kb/HT1719
If it's more than a few years old, depending on how (and how much) you used it, the battery may be bad.
NOTE: The blinking is not related to charging. When the light blinks orange, that only means that the shuffle's disk is mounted by the system (in use), so it blinks as a warning to "eject" the shuffle before disconnecting. Blinking does not mean it is charging, or indicate battery charge level (it always blinks orange).
Make sure your USB port is working properly. It's possible that it is not providing the full power needed to charge the shuffle's battery. If you have not shut down (powered off) your computer recently, try shutting it down completely, and starting it back up. If you are using a USB hub to connect the shuffle, try using a direct USB port on the computer. Try more than one USB port.
If you have more than one USB docking cable, try using a different one to rule out a problem with the cable.