It sounds to me as if you have set the keys too low relative to the
grooved roller.  I have a couple of keyed organs and set the grooved
roller and keys high.  Let me explain.

Firstly, I set the grooved roller at least 2.5 mm above the metal key
comb.  This is when lifted by the combined force of all the keys acting
on the card.  This basic setting ensures that the music passes through
cleanly and also permits you to overlap books when playing one tune
after the other.  This means you do not need to lift the keyframe
between tunes.  Music books can be up to 1 mm thick, particularly at
the beginning where a label is glued, so 2.5 mm gives a small clearance
over two of these overlapping.  I only overlap by half a page when
feeding in the new tune.  This trick cannot be done on keyless organ
for obvious reasons!

You now need to consider the height to set the keys when free.  This
depends on the design of touchbox used in the keyframe and hence the
amount of travel.  All keys must be carefully adjusted to rest at the
exact same height above the comb.  Make a small doglegged piece of wood
that will sit on the comb and register the key in its free position.
You need to know what travel is required of the key in order to change
its state.

Assuming you have a pressure box type of keyframe you will lose output
when the key is depressed by a small amount, say 2 mm.  You must set
the key 2 mm, plus a tolerance, above the position it will be in when
held down by the card.  So, if you have set the roller at 2.5 mm, the
underside of the card will be at 1.5 mm, and you could set the key at
1.5 + 2 + 1 (tolerance) = 4.5 mm.  I set one of my organs at 2.5 mm for
the roller and 5 mm for the keys.  In general, set the key, when free,
at a position above the underside of the roller equal to the operating
travel of the key.  The card thickness will therefore be your
over-travel tolerance.

You can now set your rubber rollers.  There is usually no adjustment
in the height of the lower roller.  This is set by the bearings and
diameter of the roller itself.   Ideally it should be level with the
bottom of the card (1.5 mm above the bed) but slightly above or below
this is fine.  The pressure roller is set by the screws that act on
the springs above the sliding bearings.  Just wind up the force until
the book pulls through with lots of keys operating.  With new rollers
you shouldn't need much compression on the rubber rollers.

You then need to adjust the roller force, side to side, to ensure the
book tracks correctly.  This is done by very small relative adjustments
of the two pressure screws to create a slight offset in the guidance.
The book should be guided very slightly towards the back fence.  Do not
over-do this otherwise you will wear out the fence, which is usually
brass.

Start with the book equi-distant between the sides of the keyframe
and see what slight adjustments of the two screws will do to the book's
travel.  When correctly adjusted, the book should travel very slowly
towards the fence and rest against it with a small force, leaving only
a witness rather than a groove.

It is important to take your time when setting up a new keyframe.
Your reward will be in the quality of the music and the reliability
of future operation.  It will also minimise wear on your books.

With best wishes,
Nicholas Simons, GB