Hello Les,
Are you certain about that?
I don't have Hauptwerk v3 installed at the moment, but I've just tried it in Hauptwerk v4 and it seems to work fine for me using the ExampleCustomOrgan2 organ. I also had a brief look through the source code for both Hauptwerk v4 and v3 and I couldn't spot any relevant differences - they both look correct.
The ExampleCustomOrgan2 example organ includes coupler 1216 (Choir to Swell 8 - the second drawknob from the bottom of the far left column on the screen).
Does that coupler in that example organ work properly for you? E.g. if you draw the Geigen Principal 8 on the Swell, the Clarinet 8 on the Choir and then click on keys on on the topmost displayed manual (the Swell), then draw the Swell to Choir coupler (second drawknob from the bottom of the far left column on the screen) then the Clarinet should start to play.
Maybe you have your Division.DivisionCodes switched around somewhere? (I haven't had a chance to go through your organ definition.)