On-Chip Memory instruction corruption

We have a design which uses a NIOS CPU whose instruction code is stored in On-Chip Memory. Most of the time everything works however there are times when the code is changed slightly and either the firmware consistently jumps to the beginning of the code or the code appears to freeze. This happens even when we add code that has no functional application to the system (e.g. adding debug lines to the code). We have checked the size of the memory and the size of the code and there is more the ample space for the stack. Also we have compared the contents of the Flash in which the code is stored to the code that is copied into the On Chip Memory and they are identical.

Does anyone have any ideas where we should start our debug ?