So, this season 2586 had a straightforward 4wd drivetrain, with an AndyMark Toughbox on each side. It worked wonderfully after the mechanicals put it together, all the way through practice.
However, by the end of Traverse City, our driver was complaining every other match that the drivetrain was "lagging". Being that we couldn't reproduce anything similar in practice, we dismissed it as an unknown problem that hopefully wouldn't come back. Just in case, when we got back to the shop, we replaced all of the gray Jags with black ones and stress-tested; all seemed to be well.
Flash forward to Troy. Two or three matches into the competition, we are making a terrible grinding noise. We got it back into the pit and found that one of the gearboxes was frozen. Taking it apart, a pile of metal shavings fell out. What the driver described as "lagging" was actually chunks of gears floating around inside the gear boxes.
Why did this happen in the first place? Well, as it turns out, greasing your gear boxes is highly recommended. 
Moral of the story: even if it seems like a programming problem, it can easily still be a mechanical issue.
Other moral: don't dismiss what your driver is reporting. He knows how the thing is supposed to feel, and when he's articulating that it feels "weird", even if he can't describe it, there's very likely something wrong.