Sounds like you have hot spots (air pockets in the coolant that need to work their way out). When you refill at the radiator after a thermostat replacement, the coolant doesn't work it's way through the block right away. Here is the procedure I used that worked for me.

Jack up the car as high as you can.
Loosen radiator cap.
Pull the hose at the firewall that runs into the back of the block.
With a funnel, pour coolant in until it overflows. Re attach hose to firewall.
While still jacked up, turn on car and turn heat on high. Keep revs sort of high for 5 min.
Without getting your hand chopped by the fan, squeeze the lower radiator hose 10 or 15 times.
Top off coolant, tighten cap.
Take a drive, repeat process as necessary until temp stabilizes.