Hello... depending on the finish/flatness of your heat sink... I apply thermal paste as a even thin film on both the CPU and the heat sink total surface before assembly... an stock aluminum heat sink is very porous ( not a good polished surface )... and require more than a BB size amount of thermal paste... with some cheap sandpaper and some elbow grease you can improve the finish on your Heatsink, Tape the sandpaper to a hard flat surface, and move the heatsink using your hand, using controlled even stokes, change GRIT size and repeat... aluminum or copper sand/polish very easily.
Thermal Paste is just used to fill in the surface voids between the two metals... but not as good as direct metal to metal contact.
have you tried running HWMonitor in Windows and see what your CPU core temperatures senors are reading? are they balanced between the cores? Look at what your fans are running at under different situations... a faulty temperature sensor or fan speed/Tach feedback somewhere could cause your problem.