Good question Neal
Also, are you using Analog Encoder or Quadrature Encoder?
If you're using Analog encoder be sure to update your Talon to 1.4 and also read the workaround for Functional Limitation 21.17 in the Talon SRX Software Reference Manual.
CANTalon defaults to Quadrature Encoder for the feedbackdevice. Follows the steps in Section 7 for selecting the feedback device (Sensor) and follow 7.4 for selecting the sensor direction correctly.
Use the Self-Test (section 2.4) to see what's going on in the Talon.