Hello,  It is quite true that organ pipes will often "pull" together
when tuning, though the results are not really predictable.  It most
often happens when you are tuning an 8' stop to another 8' or a 4' to
another 4' and so on, and especially when the pipes are close together.
You can tell they do this, because there will be no beats when the
pipes are played together, then as soon as they are played with other
stops, they will be out of tune.

The best way to tune is usually to tune the 4' stop (if available) to
a tuner, then tune the 8' stops to the 4'.  You need to make sure that
the tuner is adjusted to compensate for temperature changes, or you
will end up with the pipes either too short or too long (and the pitch
too high or too low).  Hope this was helpful!

David Schroth