GA-Z77-D3H won't shutdown or boot properly

Hi.

So I built the following computer for a friend...
Gigabyte GA-Z77-D3H
i5 3570
Samsung 840 Series 120GB
Kingston HyperX 8GB
Silverstone Strider Plus 600W
Corsair 200R
W7 Pro 64 Bit.

Everything seemed fine when I set it up at his place. He then told me that he was having problems shutting down and turning on the pc, so I told him to bring it back to my place so I could check it out.

I realised that I had put the PWR front panel connector on the wrong way and I thought this must be causing the problems. No, not that easy.

So after fixing this, I noticed that when the computer was shut down, the PWR led and all the case/cpu fans would stay on like it's in standby. I could then sometimes hit the PWR again and it would turn off (other times this wouldn't work and I'd have to flick the PSU switch). After that, when I went to turn the computer back on nothing would happen. I then had to unplug the PSU and wait a few minutes before trying again, then it boots.

So I thought it might be a BIOS bug, so I tried updating the BIOS, but when the Q-flash tries to do a power cycle, it just turns off and stays off. I also tried resetting the CMOS, but still no luck.

So if this is something that an updated BIOS can fix, is there someway so make sure it finishes the flash?

I figure otherwise that either there is some windows or bios setting that I've missed that I need to change (strange to be on by default) or get an RMA.

It's just a mystery as the computer once it's on works fine, and I really would like to avoid an RMA if possible. Can anyone offer any advice on what to try 1st??

Thanks