Random reset in Nios II

Thinkig better to this problem... I don't know what kind of software is running.. If you have some kind of complex software project (bootloader, kernel) it can be a problem like this:

think about a code that in some point it copies itself somewhere else (it relocates itself) and for an error in the linker script, some portions of software collide (and the first copied goes over another); if the one which is overwritten is the one that manages interrupts or exceptions, you may have the initialization procedure instead of the service routine for some irqs. This happened to me some months ago.