I have experienced similar... the bathroom register (right above the furnace) put out the most with the hall (about 3 feet away) next and the two down in the living area next to none. To get any heat in the living area, the bathroom and bedroom had to be roasting.
First, make sure your furnace is properly closed-up in back. There is no ducted cold air return - it just draws from the space its in through slots ahead of the heat exchanger and pushes back out through the plenum and the octopus of flex ducts at the interior end. There is usually a slotted panel on some part of the cabinetry that allows air from the interior to be sucked into this utility space from which the furnace is drawing.
On my unit, one side of the plenum cover had come undone (screw loosened and the pressed 'nut' had fallen out and disappeared). It was popped open a couple inches on one side. So the air in the utility space just kept getting recycled and there was very little pressure left in the plenum for the ducts so only the shortest ones (the bathroom and hall) got any warm air at all. Opening the cabinet doors to the utility space also resulted in lots of (uncontrolled) warm air that was blowing directly out of the plenum - this was the dead giveaway.
So, anyway, I removed the carpeted panel in the basement on the off-door side and the problem was obvious. One self-tapping screw later and that was fixed permanently. Also a good time to check that all the ducts are properly attached too (one was loose).
While in the basement, I also took the time to seal all the joints on the two boots there with my favorite duct tape (Reflectix aluminum tape). and make sure the basement vent was closed. Since the utility space and the basement are pretty much the same airspace I don't think there's ever a need to have that vent open.
Second, you can get registers with dampers in 2x10 size. I don't know why FR doesn't use them to allow you to balance the heat, especially since the duct lengths are so vastly different. Home Depot carries them although not every store stocks them. It seems that only areas where the heating or cooling needs of a house could get by with 2x10 registers have them in stock... I could not find them in Atlanta or anywhere in Florida but they were in stock (just two of them) in Statesville NC - maybe they will do 'ship to store' if they are not stocked in your area. That made a BIG difference in being able to balance the airflow.
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