I would not think that Hauptwerk is the total problem. I had the same issue with a Galanti organ that would play an Allen tone generator with ease but Hauptwerk had multiple hanging notes. The same setup on my current organ doesn't have the problem. I never was able to fix the problem and would like to figure it out since i have an organ that is midi but will probably have to re-midi it. I figured that Hauptwerk is just a little more sensitive than other traditional midi tone generators.
Matt