I have issues with Arabic script inside a PDF document created by UFPDF, that is an extension of FPDF that supports unicode fonts. I have correctly converted Arial font to t
May be you need to check http://www.ar-php.org/Glyphs-example-php-arabic.html
Ar-PHP library gives the ability to use UFPDF, and fixes the separate characters using Glyphs classes (part of the library).
You need to download the library to check the pdf example, as it is not listed in the website.