Looks like it is falling back to USB on SPI boot failure.
Is the same issue seen on windows as well?
Please try to reprogram the firmware on SPI flash.
SPI boot fails under the following conditions:
1. SPI address cycle or data cycle error
2. Invalid signature on FX3 firmware. Invalid image type
The PMOD[2:0] should be 0 Z 1
You can also check the flash contents using the vendor command 0xC3 from USBFlashProg example (check Readme.txt in the project).
When the boot fails and enumerates with PID 00F3, Program the USBFlashProg example from the FX3 SDK to the RAM using the control center in linux or windows and read the first few bytes of the SPI flash.
The first two bytes should be 0x43 and 0x59 which is the "CY" signature and the 4th byte should be 0XB0.
Please let me know the contents (first 15 bytes) of the flash on the failing board.