QuarkXPress® requires AXt fonts and Layout Ltd’s ArabicXT™ extension for setting Arabic text. AXt fonts are non-Unicode fonts, using the ‘Mac Roman’ encoding; Arabic glyphs are substituted for the Roman glyphs, so for example ‘alef’ replaces capital letter G. The AXt Fonts are designed to work only with ArabicXT™, and can contain only 256 glyphs. AXt is an older format not supported by other applications.
TPTQ Arabic offers Unicode compliant fonts, which is the new standard for publishing. Unfortunately Unicode OpenType fonts don't work correctly in QuarkXPress® with ArabicXT™.
We recommend using Adobe InDesign ME which supports Arabic OpenType fonts well. If you have no other option but to use AXt fonts, you could request format conversion.