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:
--- Quote Start ---
Using cable "USB-Blaster [USB-0]", device 1, instance 0x00
Processor is already paused
Reading System ID at address 0x00081030: verified
Initializing CPU cache (if present)
OK
Downloading 00040000 ( 0%)
Downloading 00045CD0 (71%)
Downloaded 24KB in 0.4s (60.0KB/s)
Verifying 00040000 ( 0%)
Verifying 00045CD0 (71%)
Verified OK
Starting processor at address 0x00040184
--- Quote End ---
I've checked BSP parameters, the stdin/stdout/stderr are all set to uart_jtag, but the console screen is empty.