Matthew Caulfield  could try the electronic tuning software from Dirk's
website:

   http://www.dirksprojects.nl/index.php?Lan=english&Page=base/home.php

Bill Chapman is right that pipes that get close in pitch or the har-
monics of each other could cause the less dominant one to change its
frequency.  This can also be measured by Dirk's tuner by switching on
and off the suspicious pipes.

For tuning my Frati Hymnia orchestrion, I use my Yamaha PSR8000
keyboard and tune to zero-beat frequency.

Kind greetings,
Willy van der Reijden,
The Netherlands