Encoder Problem

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.

Are you sure both Jaguars are seeing A and B the same? If A and B are switched the Jag will think it is indicating the opposite rotation.

How long is the cable?

Has anyone else out there fanned out encoder signals?

Are the motors wired to turn the same direction?

We checked A and B and they are fine.

The jaguar behaves as expected without any encoder plugged in, but behaves erratically with it plugged in.