You might not have had good thermal conduction from the APU to the heatsink causing the APU to run hot until the heatsink seated in better.
Did you remove the old TIM and apply new? All you need is a very thin layer of TIM to fill the scratches or low spots in the heatsink and heat spreader surfaces. More TIM is definitely NOT better as TIM is a thermal insulator compared to metal-to-metal contact.
Technical ignorance is NOT a destiny it is a choice. Do your homework so that you can make technically informed decisions and not be duped by advertising hype or mis-information stated as fact when its not.