Hi Sam,  If I read you correctly, the valve _does_ seat and the note
works 'properly' at higher vacuum levels.  If that is the case, the pouch
to lifter clearance in the secondary valves may be too shallow.  In fact,
since that is the easiest thing to do, I would try it first.  Just turn
the lifter down a full turn and try it again.  If that doesn't get it, I
would suspect a slightly warped secondary intake valve facing, Next, I
would suspect a slightly warped valve plate (cap).

Lastly, I would suspect anything which could prevent the secondary valve
from seating 100% at low vacuum.  Maybe a small amount of shellac
'dripped' down the inside side of the valve plate when it was installed.
Unfortunately, the only way to know for sure is to remove it and check.
(I don't like having to pull apart my own new work either but some times
I must, too)

Musically,

John A. Tuttle "Self-Playing Pianos"    http://www.PlayerCare.com
407 19th Avenue             Pri E-Mail: JohnTuttle@PlayerCare.com
Bricktown, NJ 08724      Secondary E-mail:tuttleja@concentric.net
"We Keep Your Music Rolling"     Authorized QRS Music Roll Dealer