If the fan speed dropped, then the heat transfer is better than before...it might not be as good as it could be, but it is better. The heat you feel is probably the heat going into the heatsink that was previously getting stuck in the chip. Also, the fan cools more than just the two chips...so if the fan speed dropped, everything except those two chips is probably getting warmer.
The best of both worlds? Apply the thermal compound correctly and then build/buy a fan controller.