A few bits of key information are missing:
- You're programming into an EPCS right?
- Have you pointed the Reset Address of the processor at the epcs_controller?
Also, you need to post the exact commands you're using for this flow. There are switches on these commands (particularly elf2flash and sof2flash) which are mandatory for code residing in EPCS (serial flash) devices to function.
Finally, you should _still_ be able to connect to the Nios II processor to see where it's at or "thinks" it is (which address does it think it's running from)...
[UPDATE]: do this last step by connecting to the processor with the IDE without downloaded code (just "connect": It's an option in the launch configuration for the debug session that you can setup in Eclipse)
Cheers!
Brendan