Ok i have a homebuilt system i am using a thermaltake m9 case with phenom IIx4 3.2ghz black edition cpu not overclocked with 6 gigs of ddr3 memory and msi 770-c45 motherboard. i installed a corsair h50 water cooling system yesterday with no problems pc was up and running no issues at all. Tonight i wanted to see how the new water cooled system did temp wise with my cpu so i ran prime95 test set the test to run it ran for 5 seconds and my pc shuts down and the power light on my case starts flashing. SO i unplug the pc plugged it back in. after about a min I tried turning the pc on it will not power on. I can see the green light on my pci lan card pop on for about 1 sec and then right off. Nothing powers on. So i figured maybe the power supply blew out so i put my other one in and still nothing. Now my question is did the mainboard blow out on me or could it be something else. I checked and rechecked all connections they are all fine. Any advice would be greatly appreciated.
I had a very similar issue with an Overclock, which ended up being the motherboard blew and took my CPU / PSU with it. I did an overclock, got the system to boot just fine, ran Prime95 and 5 seconds in... system shut down and wouldn't start back up.
Since you have tried another PSU with no luck, it looks like a more serious issue (motherboard). Have you tried resetting the CMOS and try the new other PSU again before you go looking to RMA other components?