|If you DID NOT unclamp the heat sink , don't do it now !|
If you DID unclamp the heat sink but it's bond to cpu has not been loosened such that the heat sink can move, don't unclamp it now !
Thermal compound or thermal grease or a thermal pad does not spontaneously stop working !
Attempting to remove the heat sink from the cpu when you don't need to can cause you problems you didn't have before !
DO NOT attempt to remove the heat sink if it will not break loose from the cpu when you have unclamped the heat sink and you press straight down on the heat sink and try twisting it sideways on the cpu. If it's stuck to the cpu the thermal compound will still work fine !.
In some cases thermal compound has hardened and it's as if the heat sink were crazy glued to the CPU. In that case you can't remove the heat sink separately, and on newer mboards you usually can't release the lever on the cpu socket to unclamp the cpu because you can't remove the heat sink and it's in the way.
If you can't move the cpu socket lever that unclamps the cpu when the heat sink is in the way, the only way you can remove the stuck together heat sink / cpu assembly is by pulling straight up on the assembly which can easily damage the pins on the cpu or damage the closed cpu socket. .
If you DO remove the assembly that way, if you can't pry the heat sink off the cpu, and if you can't move the cpu socket lever that unclamps or clamps the cpu in the socket when the heat sink is in the way, you can't re-install the assembly properly !
I have removed a few older stuck together heat sink / cpu assemblies, on older mboards when I was able to move the cpu socket lever to release the cpu because the heat sink was NOT in the way, but I found it was impossible to pry the cpu from the heat sink (e.g. I broke several heavy duty single edge scraper / razor blades attempting to do so), at least not without risking damaging the cpu, so I left it as it was,. and those cpu ./ heat sink assemblies still cooled / cool the cpu fine.
If you DID remove the heat sink from the cpu, you may have not installed the heat sink so that it is sitting flat on top of the cpu.
Unless you tried booting the computer many times one time after the other....
Re-using thermal compound or thermal grease will NOT cause the problem you're having with the mboard shutting off in such a short time. Even having nothing at all between the heat sink and the cpu will not cause the problem you're having with the mboard shutting off in such a short time.
The cpu would have to be running long enough for it to overheat - if the heat sink is sitting flat on the cpu that will take longer than you're experiencing for the mboard to shut off.
Thermal grease - pure silicon grease with no additives - whitish, translucent, nearly clear when in a thin layer - can be re-used, if it's clean - it never hardens. Thermal pads should not be re-used - the remains should be scraped off and be replaced with thermal compound or thermal grease or a new thermal pad . I don't recommend re-using thermal compound because even if hasn't hardened it may harden in the future and be as if it's crazy glued to the cpu.
I never use thermal compound anymore - thermal grease has never caused me any problems - it never hardens.
I have always been able to break loose the bond of thermal grease or a thermal pad when I unclamped the heat sink and pressed straight down on the heat sink and twisted it sideways on the cpu, but I don't recommend using thermal pads.