If you replace the computer plug in the master outlet with an item that you know for sure stops drawing power once turned off, does it behave correctly? Just do a quick check of this to see if it is functioning correctly. If it does, plug your computer back into the master outlet and adjust the (voltage?) sensitivity screw located on the side. On my last bartop build, I had to play with that screw for around 10minutes for it to behave correctly. You might have already tried these suggestions, you just didn't mention if you did or not in your post.
What mobo are you using?