Hi Thomas,
Are your keyboards velocity-sensitive? You may need to set Hauptwerk's keyboard velocity setting to zero to eliminate the problem you describe.
Right-click on each keyboard in turn, choose "Adjust MIDI/trigger settings manually" then look for the "Velocity Sensitivity %" setting.
If this value is set to zero, the keyboard will respond with a simple on/off response regardless of key pressure. The greater the value the more sensitive the response.
Also, which sample set(s) are you using? Most sample set producers don't use velocity sensitivity in their instruments, but a few include it to emulate the response of mechanical key action. If the velocity percentage is set too high this can lead to an unnaturally slow attack.
For some sample sets (eg: harpsichord, clavichord) some touch sensitivity may be useful. Theatre organ sample sets employ velocity sensitivity to create second touch. However for the vast majority of classical organ sample sets I find that a keyboard velocity percentage of zero is appropriate.
Andrew