If you have a tank drive system with PWM, and forwards and reverse have been swapped, but turning right is still turning right and turning left is still turning left, the left and right signals got swapped. This could have most easily happened:
- in code
- along the pwm lines
- between the speed controllers and the motors
As you have four motors, it would seem more likely that the change was in code or where the PWM lines connect to the RoboRIO, or at some connector halfway along the wire from the 'RIO to the jaguars, perhaps where you switched from a single cable to a wye cable.