No, it shouldn't have. I've installed big coolers with the mobo still in the case and gotten optimal temps. If anything, that rubbing helps spread the paste. Maybe your cooler just came with some really crappy grease. Try some arctic silver 5. Also, check in your bios to see if the fan speeds are set too low on the cooler. Some motherboards automatically rev up the fans when the temps increase, some come with preset options. You may also try the program speedfan, which allows you to control your various fan speeds from the OS instead of the bios.