Problem with Peripheral Communication

Judging by your description this peripheral is a FIFO?

When you used component editor to import the logic did you specify a native or memory type? Unless the peripheral is actually memory then you would probably want native addressing.

Assuming you go with native addressing, are you bypassing the Nios II data cache? (if you have a data cache that is)

Have you tried to capture the signals either using an external LA or SignalTap II? (looking at the signals may shed more light on what you are seeing).