Talon SRX Encoder Signal Processing Trouble

[entertainr]

Recently my team has decided to switch to Talon SRX controllers. I've been moving slowly towards working with the PID controls on them, but I have a problem. Whenever I run the motors forward, the encoder counts backwards. When I run the motors in reverse, the encoder counts up. The CTR Reference Manual labels this as a problem if I want to use the closed loop features. I have attempted to use the SetReference.vi as suggested in the manual with no success. I am using a Grayhill 63R 256 count digital encoder. The wiring has been done correctly from the Grayhill to the breakout board.

http://www.grayhill.com/assets/1/7/Opt_Encoder_63R.pdf