What you're seeing is normal so that won't be the problem.
Right at the beginning is the reset code (a little bit of a pain, but at least it's smaller then the big vector table that NIOS I had).
It's been a while since I've read this one. How do you know it's not coming out of reset? Are you trying to download the code,
and you get an error message? (make sure you turn off the system ID thing in the downloader if you don't have that core attached).
Need a bit more info on what you are trying to do (if you get an error message from the IDE post it since I've managed to cause
them all hehe).