problem when program is running in IDE

Sounds like a problem with the hardware design.

- Check to make sure you have the correct timing for the memory you are targetting.

- Check to make sure you have the proper board layout for the memory that is giving you problems (traces, shorts, solder balls on the pins, etc...)

- If you are using a Nios development board make sure Unused I/O are set as input tristate pins

- Make sure you are meeting timing in your design and have taken offchip timing into consideration

Those are a few things that pop to mind. If that doesn't get you through the woods post again and hopefully someone will think of a solution for you.