Having some familiarity with the behavior of light I can only say that
your setup is probably the source of the problem.  Rather than trying
to modify the paper would it be possible to change the scanner?  If
your scanner was working in a reflective mode (with the light source
on the same side of the paper as the phototransistors, the transparency
of the paper would much less of an issue.  Also using an incandescent
light source with infrared transistors could make scanning any type
of paper product difficult since the incandescent light emits so much
infra-red.

I would suggest trying to adjust the intensity of the light source
(sometimes brighter is better than dimmer but I think I would start
with dimmer in this instance), reducing the sensitivity of the tran-
sistors (maybe some sort of colored plastic -- bluish or greenish --
over the phototransistors could serve to reduce their sensitivity)
or trying a florescent light source (neon or cold cathode tube would
probably work best).  Theatrical lighting suppliers have a wide variety
of translucent colored material available for a very reasonable cost.

Good luck.  I'd be interested in hearing how this works out.

Bill Budenholzer
bluemax@esmrahd.com