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This the error message that appears on console
verifying 00040000 ( 0%)
verify failed between address 0x40000 and 0x4655f
leaving target processor paused also it appear a window that contain
problem occured downloading elf process failed. --- Quote End ---
So what is at that address? On-chip memory, external memory? Do you know that memory works correctly?
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I don't try to use a modelsim, because i don't know how can i use with nios-eclipse.
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If you are serious about doing FPGA development, then you need to learn to use all the tools. Modelsim is very useful for confirming that your system works, before you try to debug in hardware.
Cheers,
Dave