The secondary valve problem that you described sounds very much like
a situation that I encountered a number of years ago.  It was a real
bear to diagnose, since everything had a completely normal appearance
when the stack was taken apart.  The problem turned out to be excessively
soft or compliant leather on the lower seat of the secondary valve.
When the valve was activated, the leather was formed into a dish-like
shape, so the valve leather's outer edge maintained a fairly effective
seal against the lower seat even while the valve was activated, the
leather being held in the dished condition by suction from inside the
stack.  (I know this isn't a physicist's explanation, but it's concise
and easy to understand.) The result is, of course, that suction is not
communicated to the pneumatic as it should be.

If the leather has much stiffness at all, the problem won't occur at
very low suction levels, but will show up when suction is great enough
to pull the leather out of shape during valve activation as described.
The metal disc on those valves is supposed to help keep the leather
flat, but deformation around the edge can still occur if the leather
is too compliant.  Also, too short travel of the secondary valve does
not help matters.  Check to be sure that the valve travel is sufficient,
the metal disc is properly installed, and if necessary, replace lower
valve leather on the offending valves with a stiffer product.

                                          Dave Saul