If missed steps are a very rare occurrence, then I doubt it's the PC. But whether it really is or not, can be extremely difficult to track down, especially when it's not repeatable.I think any missed steps would have come from the computer.
From my experience, acceleration has more effect on missing steps than velocity, as much more torque is required while accelerating. Try lowering the acceleration 10-20% ans see if the occasional missed steps go away.
Increasing the pulse width in motor tuning a little probably wouldn't hurt, depending on what it's currently set at.