My board needs to be warmed up a LOT in order to work?

I’d also check that you have sufficient power (maybe ~5 watts). Try every USB 3.0 port on your computer (not all are equal in terms of power, and noise) and maybe also unplug all other USB devices while trying to update the flash. My guess would be that while attempting to write to flash the device requires extra power, than for normal operation. Have you manually tried to program the flash using LimeSuite GUI, does it say that it has Programmed X number of bytes to the SPI flash. And if successful does “birstream from flash” correctly load the contents of flash into to the FPGA ?