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I have replaced the DDR2 memory with on-chip memory (262144 bytes), but the issue somehow was 125MHz clock. I have set the 50MHz clock instead and the Nios started.
The 125MHz clock was running for sure, I have made a blinker which works either with 125MHz clock or with 50MHz clock.
The development board is Cyclone III Host board from Altera (2 clocks on board + SMA IN)
Now the strange problem is that the console doesn't show anything. It runs the CPU:
I've checked BSP parameters, the stdin/stdout/stderr are all set to uart_jtag, but the console screen is empty.
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I know this was quite a while ago, Socrates, but I'm having this same problem now. I'm wondering if you were able to solve this issue of no output on the Nios Console.