Cannot access memory at address xxx, stack overflow management ?

Are you sure the "Cannot access memory" message is not generated by your application?

Maybe in the code routines you didn't wrote. I'm not aware of such a message in standard Nios drivers.

Are you using a OS?

Anyway, before all you must be sure your hw is ok. So it's correct you now focus on checking timings, especially if the error appears randomly.

You can try loading a simple application which runs in internal memory and extensively test external memories data transfers.