I had the same problem on V26 on windows with the pipe organ. I also notice for odd reasons finale would use the sustain pedal on the pipe organs as well.. The only 2 work arounds I found is to load the MIDI files into a DAW and erase all the midi cc 

that is not part of the organ. The other option is to record myself playing it on the DAW. 

Thanks.  I do not understand DAW - new to MIDI.  I seem to be easily confused by MIDI as the terminology is not really obvious.  For example, key velocities are really volume from what I understand at this point - makes no sense to a musician where velocity is speed.....

Note velocity is volume, but only when we're talking about percussive or plucked instruments such as piano or harpsichord, pizzicato strings and so on. With woodwind or brass and with bowed strings it's the initial force of of blowing or bowing, the actaul volume of the note is then controlled by breath or expression.

Although, with the Garritan ARIA player, it can be controlled by controller #64 otherwise known as the modulation wheel.

It is worth going to the Garritan web site and downloading the manual (in pdf form) of Garritan Personal Orchestra 4.

You'll find it here:  https://makemusic.zendesk.com/hc/en-us/articles/115010742428-Downloadable-PDF-Garritan-User-Manuals

Try beginning at page 29.

JohnG