Hi Bill,  Maybe I am telling you something obvious, but here goes.
(If you suspect that they rearranged the scale to use one type of
roll on a different type of organ, that's another matter.)

I have restored quite a few barrel organs and I can tell you that
they are _never_ in the scale you'd expect or what's marked on the
instrument, at least not by today's standards.

The problem is sort of like Robbie stated.  The notes used in the past
are seldom (more like never) referenced to the A=440 Hz scale we use
today.  Each producer used what they thought best.  The least of this
problem is the fact that the standard pitch was lower than 440 hertz
until recently; the longer ago, the lower the standard.  I find organs
tuned 1, 2, and sometimes 3 notes low.

Try this approach.  Make a graph (on quadrille paper) with the full
scale of notes across the bottom (X) axis and the vertical (Y) axis,
maybe 3 or 4 octaves.  Start with the same note at the origin of each
axis and on every interval put a note.  Use all the natural notes and
each appropriate sharp.  For instance:

 A A# B C C# D D# E F F# G G# A A# B  etc.

Now, on the X axis, highlight the notes of the scale marked on the
organ.  Use a highlight marker or just circle them.

Put the pipe stoppers, etc., back where you found them as much as you
can.   Then, for each note you have highlighted on the bottom axis,
plot the note it actually plays on the Y axis of the chart.  Use the
'cents' scale on your tuner and estimate between notes, e.g.,
+25 cents = 1/4 note high.  Use a different color for each rank of
pipes.

When you're done, I think you will find that all the pipes fall on or
close to a single straight line which is at 45 degrees to the main
axes.  Some of the pipes will be off the line and you can tune them up
or down a little until they all line up.

Lastly, extend the line until it crosses the Y axis.   If it crosses
at the origin, the organ will play in the scale as marked.  If not,
the number of notes (where it crosses) below the origin is how many
note increments the organ is tuned low.  Just highlight the notes on
the Y axis that match the notes on the X axis and you have your new
scale.

A few years ago, I had an organ which played tunes that were
impossible to recognize.  My friend Jeff (who is one of the few people
I know who can tune and adjust a barrel organ or piano to perfection)
and I couldn't figure out what was wrong.  It was a 20-note organ so
there weren't a lot of notes to make music with, so, at first I didn't
bother to make a chart.  Finally I gave up and plotted it out.  Sure
enough, _one_ note was out of tune quite a bit -- right in the middle
of the melody.   I tuned it correctly and wonderful music came out.
Amazing!!!

Hope this helps.

Craig Smith