It pretty much points to it being a hardware issue and makes even more sense on the hard drive, if you restart, the hard drive is already powered up and running, when you start from shut down it takes more to get it up and running... Which could also be caused by a faulty power supply... might be worth checking it out, for help on doing this see:
http://www.experts-exchange.com/Hardware/Q_22080755.html#18064567