MAX 10 weird behaviour

Thanks for your answers,

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What memory initialization option do you use?

Do you use .sof or .pof file to program MAX10?

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I use the default options (non of checkboxes checked).

I tried programming both files.

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Have you got timing specs for the entire design? Do you have any custom asynchronous logic?

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No and no.

I can now verify that .sof part is works always and apperantly is not the problem.

It is the .hex software part that only runs fine when I use debug/run from Eclipse, but not from the generated .pof to which I combine the .sof and .hex files after arbitrary changes.

It seems like the internal flash is written properly (how can I verify it though?), but it doesn't load into memory.

Can I program the .hex file separately? how?

Thanks, Eyar