Firmware builds from the same source code differ in operation

What do you mean by different results? Different tool versions, different seeds, different os will always produce different results. But with good practice synchronous code and good timing specs, the different build results should function the same.

By Different results I mean the build in one PC always works (expected output comes) while another firmware fails at times. Using the same version of Quartus 14.200. But there is the OS difference . The firmware built in Windows 8 works whereas that in the windows7 fails at times. And by different seeds what does it mean exactly?

It sounds like you don't have a fully synchronous design, or poor timing specs. Is the design fully synchronous? Have you got full timing specs? Without then I'm not surprised the design is different each time.

I will check on the timing specs again I guess this could be a the major cause of the problem.