This is a font problem. Unfortunately, there is nothing you can do about this after you combine the files. You may be able to fix font problems using the preflight tools before, but this may not work in some cases.
I've been trying to get some sample files to experiment (and hopefully come up with a reliable solution) with for quite some time. Would you be willing to provide me with the two source files that result in the missing characters when merged? You can email them to me (my email address is on my profile page).
Karl Heinz Kremer
PDF Acrobatics Without a Net
PDF Software Development, Training and More...
http://www.khkonsulting.com