After refilling the cooling system, sometimes an air-pocket can get trapped under the thermostat, which will prevent it from opening, even when it's hot (the air doesn't transfer heat nearly as efficiently to the thermostat as water does, so it doesn't "read" hot enough to open.) Does it sound like that's what could now be happening?
Common practice is to drill one or two small holes in the side flange of the thermostat, to allow air to escape to the top of the radiator and out as the water circulates.
Otherwise, sounds like just a lot of flushing is necessary.
-Michael
