I think your speaking about the circulation blower and not the draft blower. I had the same issue and I raised the temp setting on the blower control slightly. This also made the air from the register warm, as the low temp air was cooled by the run through the basement.
I have mine connected to a thermostat, but if you just use the on/off timer to control heat you may want to leave it or not? Of course you should consult the MFG before changing anything.