Thermally related effects are often associated with firmware not making timing (not achieving timing closure) on the hardware in question when either hot or cold. This can cause the effect you are seeing.
Try loading Protocol 1 firmware and see if you have the same problem. Thetis will run with P1 firmware but only at 192KHz sampling rates. If you don't observe the same problems with Thetis and P1 then you'll have to go on a witch hunt to see if you can find a version of the P2 firmware that works reliably on your serial number hardware.
The reason that P1 firmware may work where P2 might not is primarily associated with timing closure on the Ethernet PHY interface. At 100Mbit/s timing closure is easy. At 1Gbit/s not as easy.
It is strongly recommended you use Bootloader to make firmware changes. If you need help with this start with reading the tacked topics here:
viewforum.php?f=18The latest P1 firmware is in the TAPR repository. The latest P2 firmware is here:
viewtopic.php?f=32&t=3192