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Strange max 10 startup & non-volatile operation

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I have a PCB I made using the Max 10 10M16DAF256C8G dual supply series FPGA. I've observed some unexpected behaviors in terms of startup and non-volatile operation.

When programming the board with .sof file, everything worked okay the first time.

When programming the board with .pof file, I had to play around with tools -> options in the programming window and check the "initiate configuration after programming" box for the program to work. I'm also not 100% clear on whether it should be CFM, UFM, both, neither. According to this https://www.altera.com/content/dam/a...m10_config.pdf, it reads like either one will work to program into internal flash.

The problem is, the non-volatile behavior in both scenarios appears finicky. After the board is programmed, shut down, and restarted, I have to wait some random amount of time before it runs the program. Sometimes it takes maybe 5 seconds, other times it might take over an hour. The program is a simple program that turns on an LED and some other stuff. I don't know what might be causing this - if there is a certain power-up sequence this thing needs to see or what, maybe a setting somewhere in the programmer?

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