Solution
Thermal shutdown occurs at an FPGA temperature reading of 98 degrees Celsius. We chose this number based on the operating temperature range of the FPGA (max of 100) minus the uncertainty of the FPGA temperature sensor (+/- 2 degrees). Of course, we normally don't expect the FPGA to hit this temperature, given proper chassis airflow and slot blockers in any empty PXI slots.
The RF In and RF Out temperatures cannot cause thermal shutdown, they generally run cooler than the FPGA temperature.