ATU triggers two flashing lights

Burt,

2 flashes indicates the SW is crashing in the radio,   as per the HW Reference Guide,

Error Conditions
Certain hardware and software error conditions cause the radio to stop operating and display an error code by flashing the Power button light as follows:

• One red flash: Fan malfunction
• Two red flashes: Software crash
• Three red flashes: Boot failure
• Four red flashes: Input power over voltage
• Five red flashes: CPU overcurrent
• Six red flashes: Input power under voltage

In the case of a software crash, the error code repeats for about 15 seconds, then the radio will reboot. In the other cases, the error code repeats until the Power button is pressed, then the radio shuts down. An additional press of the Power button is needed to restart the radio.

Too much RF inside the box,   have you tried to a good known dummy load?  
On the correct antenna port?
If you lower the RF output is there a point that transmitting does not crash the SW?  

Could be local RF conditions (Antenna or Common mode RFI )    or a HW issue in the radio..  

Let us know what you find,

Dudley