Hello Paul,
Thank you for posting and welcome.
What kind of scanner are you using?
What version of InfoPath are you using?
Is this a browser form or a filler form?
We have developed forms that use scanners and we have never experienced deleted characters.
Maybe there's a rule on the field that deletes it (hard to imagine though). What are the character limits on the fields? Don't forget you have the C and the B.
Sorry I couldn't be more helpful.
Patrick