Wow you guys find the most interesting problems! Sorry to hear it though. Do me a favor and try updating the firmware. I made some changes recently to the IR detection and clock set routine.
Firmware:
https://github.com/Jerware/GameFrameV2/tree/master/firmware
Firmware update tool:
https://www.pjrc.com/teensy/loader.html
Please let me know if that fixes things!