I get that on my 003 every so often when I have Analog 7-8 feeding in for SM. Just APPLE+ 2 (numpad) to open session setup, and re-click the Clock to Internal and it goes away. Every so often I her it start up for no reason so doing that same thing to reset the clock fixes it. It's either a bug with the PT firmware (I never noticed it before 8.0.6) or some issue with the clock on the 003. Not sure, my device is out of warranty and I don't feel like being nickled and dimed by Avid to get it looked into when the fix is quick (and it doesn't bother the Mains or busses, just the audio input which I hardly ever use except for Computer Audio monitoring in).
But I believe the root of the issue is somewhere with clock or how the clock is handled, and doing that command should set it straight (at least until it sneaks up again).
For what its worth, I did a lengthy post on the ProTools Ideascale and nobody gave a damn about it nor did the Avid moderators. The DUC also turned up no info on this issue either. Seems to be an isolated issue, maybe only with some 003 users.