I'm not sure but it sounds like you are using the encoders connected to one Jaguar per drivetrain side and then syncing them via the cRIO. There was some extensive discussion on doing this in this thread:
http://www.chiefdelphi.com/forums/sh...ad.php?t=89282
One thing to note is that attaching the encoders directly to the Jaguars can introduce ground loops and noise into the system, which could potentially cause the Jaguars to fault. As shown on the 4th page of that thread a solution was posted in schematic form that eliminates these ground loops and attempts to alleviate some of the potential noise issues.
Obviously I can't say for sure what is causing your issues but that thread has some great discussion on the issues with what you are trying to do and potential solutions that may help you out.
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