The same thing happens on a Kindle 3 with the 3.4 firmware. It seems that there are RTL font embedding problems
I.e. you'll probably have to wait for a PW font hack or another firmware update.
BTW, the ugly Arabic/Persian glyphs seem to come from the Code 2000
Once a font hack is available you'll probably be able to remap it to another font. AFAIK, It's possible to remap fonts on K3 without a jailbreak, but I don't know whether the same method works for a PW.
You may want to ask in the Kindle developer forum
if it's possible to remap code2000.ttf to a better font without a jailbreak.