It is most likely a hardware bug in the circuit. During our testing we realized that the Dual NOR gates used in the design are too fast, and there needs to be some propagation delay. Using a cheap NOR gate chip from Fry's did the trick. We are still trying to see if this can be fixed in the firmware.
Maybe you may also want to try to use a bigger capacitor for the phase shifter in front of the NOR gate. A circuit should not depend on the propagation delays or fabrication tolerances of logic gates. I also tried to use the internal comparator of the PIC as a NOR gate, which is even better since it has some clock synchronization register. But it has shown that the comparator is not fast enough...
Already tried using bigger capacitor. Does not work. The only work around we have found is using a slower gate, so far.