Hello,
Thanks for your reply.
I noticed that the problem was with my power. As I'm starting with our project I just simply used a 3.3V Linear regulator to power the board but it seems that it is quite power hungry at startup.
So the problem was that when the FPGA gets configured from Flash the peak in current draw is quite quick and huge and my linear power couldn't handle this, which meant that the module rebooted every time the FPGA got programmed.
This resulted in an endless loop, with reboot and so forth...
Have to take this into consideration when designing my final power solution. At least to have big enough capacitors.
br,
Jonas