This is most likely the cause of the issues you are running into; the PID controls built into ROBOTC are looking for a closed-loop system and require the Integrated Motor Encoders (IME’s) to be used. Because of this, the PID control will not work with Quadrature Encoders.
However, you can write a custom PID algorithm for the quadrature encoders for your specific drivetrain/encoder configuration. James Pearman has an excellent thread on this topic that I highly recommend taking a look at, found at the link below.