[cabmandone]

From the sequence of operation in the owners manual:
The blower starts at approximately 400-500 RPM. After
20 sec, the motor is turned off for 1/10 of a sec where a coast down
calibration is done to evaluate resistance of the conditioned air
duct system. The microprocessor then determines blower RPM
required to provide proper airflow for heating mode.

Again, I'd make sure that every supply register is open. Yeah your return duct being choked down is half assed and shouldn't exist. No I don't think the dust in the flex is causing the issue. The flex itself can be an issue if the bends aren't smooth (like pictured) or where unsupported and sagging. The furnace should be adjusting for the inefficiencies in the duct system through the coast down calibration.

One more thing: What is the code number you're getting? 44?