Cannot use "restart" since installing SSD

After much wrestling I managed to install a Samsung 830 128gb ssd. I also have 2 x1 TB sata hard drives, one connected to a sata port and one to a micron port (I tried expansion cards with extra sata ports but couldn't make them work). All works fine except if I try to restart the pc it goes into a loop. When I shut down, either through Windows or the power button, and swtich on again, everything boots as you would expect. It's not a huge problem but when I install something or there are updates requiring a restart it's annoying to forget you can't do that and get stuck with the looping until you press the power button and stop it.
Any ideas?