We have changed PDF classes and updated some files to support different encodings after version 3.1 has been released.
Package is available here http://www.viart.com/downloads/pdf_files_cyr.zip
Please upload the archive file to the root of your web folder and unzip.
 
List of updated files:
user_invoice_pdf.php
admin/admin_invoice_pdf.php
admin/admin_packing_pdf.php
includes/pdf.php
includes/pdflib.php
includes/font/cp1251.map
includes/font/helvetica.php
includes/font/helveticab.php
 
Please note.
For PHP-based generation you need to use correct files includes/font/*.php
For PDFLib generation please make sure that system fonts that you are using have support for Cyrillic (or some other necessary for you) encoding.