Help: Altera Stratix || Dsp board reset

Thank you for your comment, to to more explicit regarding the reset. The DSP development board comes with a factory default design implemented in flash. While programming the device the correct status LED's are lit up to indicate that the device is being programmed. After this the user LED comes on for a very brief moment and then the board simply loads the factory design from flash memory again. I am not sure that this problem is caused by SignalTap at all, it is simply a hunch. I have tried giving the fitter another seed, this however did not help. Could it be that some configuration file has become corrupted in the process, since when I try to simulate the system, I get an Quartus internal error complaining about a pre_simprocessor.cpp file.