Very long time to start up and then turns off

The other day I woke my computer up ( I usually live my computer running and use the Windows 7 sleep mode ) and tried to open itunes. It would not open, double clicked a few times and nothing, checked in the task manager and nothing in the applications but could see it in processes. Tried ending the process tree and it would not end. So I restarting my system, it went into the shutting down mode, after about 5 min and still said shutting down I became impatient and just held down the power button. Push it again to restart, starts up goes to the motherboard logo screen and stays there for along time, shut it off, turn back on a few times no change. Finally I turn it on and just leave it, after about 10 mins it finally gets past the logo screen and starts to work, gets to the Windows loading banner screen and stops again for long time, I go in another room and just let it run, after about 10-15min I hear the windows start up chime so I think good, finally, go back in my office a little while later and my computer is turning itself off and on at about 3 second intervals. When I get home from work I will open it up and start diagnosing it, any advice on where to start?

System Specs

Gigabyte X38 DS4
Core2Quad 9550
OCZ 8gb DDR2 1066
2x ATi 4870 in crossfire
2x 500gb Samsung F3 in Raid 0
Hitachi deskstar 250gb
Swiftech water cooling