Just a personal comment, I've been through the recent FVC and I experienced much unpleasantness when using the VEX encoder. Not sure due to its poor build quality or otherwise, there is often much plastic dust (due to friction between plastic parts when spinning) accumulating INSIDE the encoder unit, which affects the encoder's output and hence would affect you during tuning/testing and soon you will find yourself changing program values unneccessarily. The abrasive dust would get clogged not only in the optical wheel but also in the IR sensing area which results ultimately in the failure of the device to sense any rotation at all (after long runs) and you will need to open it up and blow air into it in an attempt to clear out whatever crap is inside...
One solution could be to position the optical wheel properly and suspend the optical wheel on bearings..

not sure if that helps..
In a nutshell, don't rely too much on the vex encoder
