OK.. What thermal paste did you use. From what you describe is power cycling. This can be caused by literly anything, However, I'd make a guess that you used a conductive thermal paste and that spilled onto some of the electronic components (Capacitors mainly) on the CPU package and that is causing a short circuit. This is not damaging your CPU but can cause power cycling. I always use a ceramic based thermal paste such as Arctic Silver Alumia.
Good luck and let us know.