I have and issue that the only way the FPGA on a myRIO Module runs is if it is programmed over USB. It does not run after powering down and back up. It does run after unplugging the laptop after it has been programmed over USB. I suspect that not running after a power cycle is because the FPGA is only getting the image loaded internally over USB.
Is there some special LabVIEW command to program the serial flash on the FPGA so that the FPGA runs at powerup, or does programming the FPGA over USB always program the serial Flash?
Do you have just FPGA part, and no Real-Time application? In case of just FPGA part, it is enough to build bitfile, and then deploy it (actually, upload it to myRIO and set to run at boot). Here is Knowledgebase article from NI about how to achieve it.
In case when you also have Real-Time part, then it should be also deployed, and set to run at the boot. Here is another detailed article about how to configure it: Deploy a Startup Application to Your MyRIO.