FOP does not currently generate a ToUnicode table in the output PDF, this must be corrected to have correct encodings in PDF. Without this, cut and paste from PDF is not correct, and search fails with non-ASCII characters. The current situation is correctly documented at http://xmlgraphics.apache.org/fop/trunk/fonts.html, under "TrueType font metrics". A patch has been provided (bug #5335, comment #9) but apparently the code comes from the FOray project, see if they agree to donate this code.
PDFEncodingTestCase added, DISABLED_testPDFEncodingWithCustomFont demonstrates the problem.
Fixed in bug #5335 *** This bug has been marked as a duplicate of 5335 ***
batch transition to closed remaining pre-FOP1.0 resolved bugs