Hmm… We’ll address the issue this week.
The issue may come from a difference in a preparing of text to output to PDF and to RTF. By RTF the Arabic or mixed script should be printed “as is”, letting MS Word to ligaturise and to render it correctly. For PDF output the text should be pre-processed to appear as a correct sequence of glyphs.
I suspect in some situations it uses the PDF preprocessing for RTF output, which is wrong. But it is only a guess, we need to analyze that in details.