[sjspry]

In your code, do you have the Jaguar objects (or similar) placed somewhere where it would be local to your autonomous routines? IIRC, the motors will keep running until set otherwise, which might be occurring (as the teleop routines don't have direct access to them).

That is the only thing I can think of, last year we used a built-in arcade drive system, which I can only assume does some sort of reset.