Robot mysteriously stopping and backing up

[computerish]

We've been experimenting with the new line sensors and coded up a very simple line following autonomous mode (our own, not the FIRST provided one). It works about as well as you would expect for 5 minutes of development and 20 minutes of testing, except for one thing. At apparently random times, the robot stop briefly and then starts going backwards.

I'd be inclined to blame it on the robot turning and putting too much power to one wheel and having that one wheel pull the whole robot backwards (this practice bot has very high friction wheels and its on carpet), but I want to make sure that there isn't some strange "feature" in WPILibJ that might make our robot back up.

So in short, is there anything in WPILibJ or in the Jaguars that could cause them to run in reverse without being told to?

Thanks!