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DDR2 pins are OK, I have taken them from a working example from development board CD.
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Do you mean you tested the example on the same board? Or is this your custom board which pin locations have been copied from the dev board?
I don't think the problem is with ddr, since debugging tools should be able to get the correct sysid even if memory is not working. IMHO it's more probable the Nios is not working.
Maybe a problem with input clock or reset signal. Are you sure the fpga has been correctly configured?
Anyway I'd suggest this simple method to exclude ddr: you can temporarily replace it with onchip memory; this is enough for a "Hello world" kiind of program and it will let you take away any concern regarding external connections.
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