Help: Altera Stratix || Dsp board reset

An internal error shouldn't have anything to do with the board failure. (That's just something wrong with the simulator and the inputs your giving it. If you can, file a Service Request on the Altera website).

There is either something in your design that initiates a reconfiguration(make sure your design has truly entered user mode, i.e. have it drive an LED in a recognizable way). If it's not your design, it's something probably at a diagnostic level(if you lose power, it will lose configuration and reconfigure from FLASH, I believe). I don't know the design or board to help anymore. Is there a MAX device that manages the configuration scheme? I believe on some boards that is the case, so the user design can tell the MAX device to reconfigure(which you might be doing on accident) or it monitors configuration status and will reconfigure from default FLASH if it thinks an error occured. These are just guesses though.