No, not the turns counter. The proper name for the theta box is the PLQ. It is mounted on the right hand side of the LCU about the same height as the fuse box.
The LX card in the LCU card cage is the servo interface. It is known to cause some weird calibration problems. Theta commands exit the LX and go to the theta box (PLQ) and out the lower I/O plate to the theta motor. All other robotic signals exit the LX, out through the upper I/O plate over the roof, down the coil to the two PLS modules.
The PLQ or LX should fix it if it is a theta problem. The theta motor is indestructible, i've never seen one go myself. Let me know how it goes.