Termite/serial com port opening can Crash Spartan 3 (stop sensor heating)

Connect USB to laptop, then powering spartan 3 on.
Open termite and connect/disconnect can stop the heater from outputting, red light turns off. No serial commands received or sent.

I can see faint flashes from the serial comms (I think 6 flashes then pause then 6)

disconnect termite and close, power off and on spartan. Repeat above process and try again and it works (or not).

I can repeat crash the spartan so to speak via the serial port.

This is on firmware 1.00.

Is this a known issue?