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IS your thermostat set to automatic on the fan switch? If so then you may have a stuck fan relay in the air handler. If it has an electronic control board the relay is on the board and the whole board would need replaced. If it is not a stuck relay then you could have a crossed wire from the thermostat to the air handle, usually the green wire from the t-stat, it could be crossed with the red wire that supplies 24 volts to the t-stat.
Sometimes a motor can start to run backwards... on an indoor fan it is usually because the air inside for some reason started the fan backwards while it was off and then when power is applied it continues to run backwards... once this happens the fan is ruined and it often will not atrt the right way even after the air problem is solved...
You will need to replace the motor and see if you can figure out why there was reversed air flow in your system...