I assembled a PC a few months ago and the USB ports on the case were a different standard to the motherboard i.e USB (1) on the case and USB2 on the motherboard. USB3 is now around, but not yet as widespread.
The case USBs are plugged into a secondary USB power socket on the motherboard and that can not always provide sufficient power for the external devices, whereas the back ones, which are built directly onto it, seem to be able to. Generally I find that it helps to use a self-powered USB extension socket(s) for those intermittently used devices.