Encoder Problem

[ehfeinberg]

We are having an encoder problem with our robot. After testing the robot yesterday, We were having major speed control problems using CAN. We are using a WCD(6 wheel drop center) with the encoder spliced going to both jaguars.
One jaguar has 4 wires going in (+,-, A,B), while the other has 2 wires going in (A,B). The speed control only goes 1 direction correctly (if the output of the jaguar is wired backwards). While going backwards, the wheel tries to spin backwards but the wheels often alternate directions creating a jerking motion. We have been able to get the drive moving with %V-Bus. Any help would be appreciated.

FYI: The jaguar LED flashing is as follows:
Fowards: quick flashing red.
No Command: solid yellow.
Backwards: quickly flashing and alternating between red and green. //The code has no issues.
The jaguar has firmware v101.