Am 01.05.2013 13:21, schrieb Muhammed F. Bayraktar:

So here is an example file. It's the one I'm working with, only the first 
sentences and a random
arabic phrase.

Hi Muhammed,

your example file contains many preamble code that may cause problems. Please only use there things you know.
For example you have

\usepackage{xunicode,fontspec,xltxtra}
\usepackage{longtable,array,ragged2e, booktabs}
\usepackage{textcomp,url}
\usepackage{graphicx,pdfpages}
\usepackage{arabtex}
\usetocstyle{KOMAScript}

All this can be deleted because LyX takes care of all these packages. If you explicitly add them to the preamble you can get compilation errors when viewing the PDF.

The next issue is that you set a graphics driver in the document settings. This is not recommended until you explicitly need a special one for your publisher.

Now comes your problem: In the document settings you may not set the language package to babel. XeTeX uses its own package called polyglossia and LyX will automatically use it but only if you are not forcing babel. The Arabic parts must furthermore in the language "Arabic(arabi)", not in "Arabic (arabtex)". (arabtex is really awful for multi-language documents and can in general not be used when non-TeX fonts are used.) I updated the Wiki page now accordingly:
http://wiki.lyx.org/Windows/Arabic

As last issue you should consider to remove the typewriter font style from your Arabic to get a nicer output.

Attached is your fixed file. (I had to use there another font because I haven't 
your installed.)

regards Uwe

Attachment: miniexample-fixed.lyx
Description: application/lyx

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