Here's an update. I've attached the profile to this post.
The setup is the same, with motors on each side, chained up to encoders:
Encoders: US Digital S5
Motors: 24V 252RPM
In open loop they run fine. The left motor is motor 1 and the right is motor 2. Due to the motors being on reversed sides I have to drive the right to a negative value to get it to move in the correct direction.
The encoders being used have 500 pulses per revolution and the motor controller is set accordingly. Encoder 1 is set to feedback to motor 1 and encoder 2 is set to feedback 2.
It's set in Closed Loop Speed Mode with the PID set to 1,2,0 for each motor. When applying power to the motors in the Roborun software (run tab) the result is an oscillation in both speed and direction and traveling no faster than 20 RPMs in either direction. The loop error detection is 1s @ 50% Error.
Now, when I swap the polarity with one of the motors, it seems to work better but the motors max out and will not stop unless I hit the emergency stop button. They also do not react to a power less than about 250 and both motors activate when one of the sliders are moved, it doesn't matter which I move.
If I tweak my setup by having both encoders set to Feedback(1,2) then motor1 seems to function properly with the motor control slider but the second motor control slider has the same effect in the previous situation (both motors go full bore and will not cease until I hit the emergency stop button).
EDIT:// Flipping A and B on the encoders seems to have fixed it.