I'm with M_C on this, It's getting confusing because your not making it clear how you are running the motors.

Regards the pulse timing I didn't suggest the BOB was to blame but rather the fact it's using the parallel port, which is very often the cause of such issues. Often PC and BOB working together to screw things up. My suggestion to go with an external controller will virtually eliminate all the issues the PP suffers from and increases performance and reliability massively.

Without knowing more about the PSU I can't say if a lack of power is the problem or not like DazP keeps chirping on about, but it's one possibility I suppose thou the fact you say it does it at low feed rates and the fact you don't have the motors tuned overly high makes me suspect this is not the cause of your problem.

I'm still putting my 10 pence on the pulse timing, but you are not clear on how you are checking this or the results you are getting so the jury's still out here until your more clear.?