so basically the air handler is in an unheated space during the winter and you run hot water baseboard for the heating.the air handler is acting like a static heat sink and chilling out being in the attic.the air even though it is not moving as in a fan running ......is actually migrating down as cold air does.if it was mounted on the garage floor just as you enter the house from the garage you would have minimal cold migration.the solution

disconnect the discharge duct and the return ducts if it is flex type right at the air handler and cap the flex......or block the main supply trunk into the house with a slide in piece of styrafoam as if a filter would slide...also cut a piece to fit in the return grill also.dampers are good if air is moving on them but when its cold out and migration is happening they are just another cold sink and looking to drop the cold air down into the lowest point......your house.extreme solutions relocate the air handler to the garage floor,heat the attic with some of that baseboard

...just kiddin' don't do anything in the rooms on the registers isolated the sources