Hello David,
[Topic moved here.]
Hauptwerk's MIDI recorder records positions/movements of the master volume slider, so if the originator of the file had it set higher than you normally do then the recording would sound correspondingly louder.
The MIDI recorder also records positions/movements of swell box pedals of course, so if, for example, your MIDI expression pedals aren't normally (or ever, e.g. due to your MIDI pedal not covering the full configured value range) as open as those of the originator then recordings could sound louder and brighter.
Also, on a theatre organ, perhaps the originator is using second touch to play a larger registration than you normally would (e.g. if your MIDI keyboards don't have second touch).
The only other thing that could conceivably be relevant is that MIDI recordings will potentially contain note velocities, which might be different to the velocity values that your MIDI keyboards would transmit. However, probably no organ sample sets would use velocity to affect amplitude (conceivably aside from percussion stops on theatre organs).