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Can anyone please tell me the problem.
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Do you have a testbench for your CPU? Have you simulated it in Modelsim? If not, its time to learn those tools.
There's not much point in going to synthesis until you know your logic works correctly in simulation.
If you've never used Modelsim before, there's a basic example in this thread
http://www.alteraforum.com/forum/showthread.php?t=32386 Try and create a testbench for your CPU, have it execute code, and see if you can track down your problem. If you cannot, then post your code, your testbench, and an explanation of the design. Members of this forum will provide advice.
Cheers,
Dave