Assuming you're using the new TalonSRX Breakout boards (TSUB-2)?
The CIMCoder encoders require pull-up resistors for reliable operation. I'd bet that is the issue you're running into. If you have the means, solder some 10k resistors into R1 and R2 on the Talon Breakout and that should solve it.
The Rev2 Talon Breakouts don't come with these by default since US Digital and Bourns encoders don't require them, but Rev3 and up do. If you don't have the parts or the means to solder them, send an email to
support@mach-engineering.com and they'll send you the parts. You can also toss the boards in a padded envelope and they'll make the change for you (email first).