Sage,
That could be a bad recommendation, depending on which version of the CNC4PC BOB he has. The earlier ones used *very* slow optos on some outputs (30-60 uSec rise times), so cannot be used for step signals at any reasonable step rate. The board is marked as to which ouputs are appropriate for faster signals, like step, and which are not. If he has the current rev of the board, this is not a problem, but with an old one, it definitely is.
Also, your conclusion in the first paragraph that "the BOB hardware is fine" is a bit hasty,IMHO. I was able to perform similar tests on my machine, and ruled out the BOB as a result. In the end, the problems WERE caused by the BOB, which acted up mostly only when multiple axes were running. It was a number of noise problems and design issues on the BOB itself. Replacing the BOB has completely cured the problems.
Regards,
Ray L.