Have you checked to make sure that all of the supply registers are open, the air filter is clean and nothing is blocking the return air grill?
It almost sounds like you could be cycling on a limit switch.
Usually on gas furnaces, the blower is controled by the onboard controls, in the cooling mode the thermostat will control the blower.
I would be looking past the thermostat, at the furnace it self.
I hope you find this helpful. If you continue to experience problems, please let us know and we will dig deeper. :)
Paul
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