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If the environmental variable is set correctly, you will see lots of messages from quartus_pgm during host execution that starts the programming process through JTAG and finishes it (which can take up to 30 seconds) and then your kernel is executed. Did you see these messages? On my environment those messages are especially printed out in green, but I use Linux and things might be different on Windows.
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Yes I saw the green messages and it took much longer to configure compares to vie PCIe.
I tried to identify what's causing the problem since it doesn't happen a lot before, but all I found so far is that it's related to storing data in buffer.
Previously it would happened maybe 1 out of 50 times, and as I store more data in the device buffer the frequency increase, now it would happens like 1/3 of the time...
Weird thing is that it only happens at the beginning of my program(video processing), sometime it happens at the 10th frame or the very first frame, but if it pass the first few frames safely then it can run all the way to the end.
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