Matthew,  In a normal Gem Roller Organ, there are three common areas
which may be leaking, contributing to a loss of vacuum.

The most common that I've seen is the bellows cloth which covers both
the bottom bellows (exhauster) and the top reservoir.  Look for any
places where the cloth has become brittle or come loose.  If so, it's
usually not difficult to replace the cloth, if you have decent
mechanical skills.

A second area is (as you mention) the valve flaps.  The outer flaps,
being exposed, are subject to physical damage.  But if the leather has
become stiff or has curled or deteriorated, remember that there is also
a second inner set which may have similar problems.  So, here's the
scoop: If the bellows cloth is bad, you'll have the organ apart so
you'll want to replace all the valve flaps.  If the flap valves are
bad (other than external physical damage), you'll need to replace the
bellows cloth to open it up.  In other words, just do it.

A third, and sometimes overlooked, area is the pads on the valve
pallets.  If you want to find whether leakage is in the bellows or
around the keys, insert a flat sheet of paper between the valve pads
and the reed openings.  As you crank (without a roller), the vacuum
will draw the paper against the openings, sealing them off and
eliminating any leakage there.  If the reservoir doesn't compress under
vacuum, check the bellows: if vacuum seems okay, check the valve pads.

The valve pads may themselves may need to be replaced, the leather
having become stiff or contorted or the felt too stiff.  But they also
must lie flat against the opening.  With no roller present, all pads
should close flat, with absolutely no leakage.  With a roller present,
the closed valve levers should just clear the wood of the roller.

The metal levers may be bent carefully to accommodate, but too much
flexing can break them, so do no more than necessary.  Notice that the
tips (which follow the roller) angle slightly to your right (as you
face the organ) so to follow the slight spiral of the rows of
pins -- don't attempt to "straighten" them!

I'll be happy to provide more detailed discussion or advice on any
areas which need clarification, or answer any other questions you may
have about Roller Organs, as that's my main hobby!

Todd Augsburger - Roller Organs
http://www.rollerorgans.com/