The are two potential reasons why your Nios II/f fails.
There is a known bug in the Nios II/f data cache in release 1.0 that shows up on Cyclone.
A fix for this bug will be released in a few weeks with the Nios II 1.0.1 release.
The bug is a rare case that only shows up in unoptimized code. So, as a quick experiment,
make sure all your code is compiled with optimization enabled.
The other possibility is that the data cache isn't being bypassed/flushed consistently by the software.
The Nios II/f uses a writeback cache so if software bypasses the data cache on a store and
then uses a normal load that reads the value from the data cache, the most-recent value
of that address won't be returned. This is not a bug in the data cache but is a bug in the software.
Can you tell me more about your SOPC Builder system and the software you are running?