gardner:
Or they could be caused by excessive noise or voltage transients, if the motor controller does not have proper blocking diodes and bypass capacitors.
The correct links are:
http://dx.com/p/l298n-stepper-motor-driver-controller-board-for-arduino-120542
http://www.geekonfire.com/wiki/index.php?title=Dual_H-Bridge_Motor_Driver
As you can see, the diodes all appear to be in place; there are even a couple of caps. Though there appears to be a large (likely electrolytic) cap missing on the board; what it is for - dunno, but you might want to look at that...
Also - does your motor have non-polarized filtering caps installed on it? Most small motors should have these installed if there is excessive electrical noise coming from the motor; basically three of these caps are soldered on: one across the terminals, and one from each terminal to the case (these may be difficult to do put in place, though - start with the single one across the terminals). The caps need to be rated for the voltage of the motor (which shouldn't be an issue; most caps are rated for much more voltage than such a small motor will see). You want something around 0.1µF; see this article for more information:
http://www.beam-wiki.org/wiki/Reducing_Motor_Noise
Also - do you have the jumpers set properly to use your external motor supply? I'm only asking because maybe the motor is still trying to be powered from the USB supply, and is causing a voltage sag or something that is messing up the USB...