If you have a foam block to put the motherboard on I'd suggest trying to run the system outside the case to troubleshoot a ground fault. Alternatively, you can use the anti-static bag the motherboard comes in.
If it fixes the issue, make sure you have the correct amount of motherboard stand-offs installed into the case, and make sure the are all in the correct location. Too many stand-offs create a ground fault that can potentially damage your motherboard and cause all kinds of issues.
I have also seen this issue come from a faulty motherboard.
Edit: I have sometimes found that re-mounting the motherboard can fix the issue, as long as you have the right number of standoffs installed and they are all snug (do not over-tighten as they strip easy). Use a 5mm or 1/4" socket to tighten them.
If the solution is not fixed by running it outside the case, strip the machine down the the bare minimum to run (single stick of ram, use onboard video if available, only the boot HDD, etc). If that does not work, then one of those base components is faulty. This may also include the power supply.