The problem reason is that recent PD4ML versions are more strict by character encoding conversion.
ISO-8859-1 (also called Latin-1) is identical to Windows-1252 (also called CP1252) except for the code points 128-159 (Š = 138). ISO-8859-1 assigns several control codes in this range. Windows-1252 has several characters, punctuation, arithmetic and business symbols assigned to these code points.
As I see you use Windows-1252 as default; PD4ML relies on ISO-8859-1.
A general solution for that type of issues is to utilize TTF embedding feature of PD4ML.
As long as you run DMS edition of PD4ML, the easiest workaround would be to enable PDF/A generation mode (make sure pd4ml_rc.jar is in the same directory with pd4ml.jar) with pd4ml.generatePdfa(true) API call.