It’s possible that what you are seeing on the LED is indicating that the software is doing a watchdog reset because it’s getting in an endless loop when trying to transfer the EEPROM data using the E2TB.

I do not know what version of TCBC software you had, but maybe it’s very old and the new GECB software, when trying to transfer the EEPROM contents, is somehow getting messed up. That is one possible cause - but of course it’s impossible to say if it is really what’s happening. Perhaps something is being logged in the error log on the GECB? Or maybe you see erratic behavior of other things like the SVT/OFT is not working.