Basically a system integration problem. Most likely,
the problem is that you either:

 A) Have FreeFont as part of your sans-serif 
    alias.
 B) Don't have any Arabic font as part of your
    sans-serif alias, so FreeFont is used.

FreeFont has the Arabic glyphs, but is not a proper
OpenType Arabic font.

I'll leave this bug open because we do need to 
eventually enhance fontconfig to ignore such
fonts when choosing a font for Arabic, but 
it's basically a fonts.conf misconfiguration
/ broken font issue.

Thanks for replying,
I don't have freefont at all
I'm using Microsoft tahoma ttf,
here is part of my fonts.conf:
        <alias>
                <family>Tahoma</family>
                <family>Helvetica</family>
                <family>Arial</family>
                <family>Verdana</family>
                <family>Nimbus Sans L</family>
                <family>Luxi Sans</family>
                <family>Kochi Gothic</family>
                <family>AR PL KaitiM GB</family>
                <family>AR PL KaitiM Big5</family>
                <family>Baekmuk Dotum</family>
                <family>SimSun</family>
                <default><family>sans-serif</family></default>  
        </alias>


and
        <alias>
                <family>sans-serif</family>
                <prefer>
                        <family>Tahoma</family>
                        <family>Verdana</family>   
                        <family>Nimbus Sans L</family>
                        <family>Luxi Sans</family>   
                        <family>Arial</family>
                        <family>Helvetica</family>
                        <family>Kochi Gothic</family>  
                        <family>AR PL KaitiM GB</family>
                        <family>AR PL KaitiM Big5</family>
                        <family>Baekmuk Dotum</family>
                        <family>SimSun</family>
                </prefer>
        </alias>

Still no effect.

If no fonts in your list of fonts in your fonts.conf have
Arabic in it, then it will pick a 'random' font on your
system with Arabic glyphs. Last I knew Debian systems
tended to have FreeFont on them.

Tahoma contains arabic glyphs, It's the one used if no xft, "can't
tell if it's the one with it or not"
freefont is not installed:

apt-get remove --purge  freefont 
Reading Package Lists... Done
Building Dependency Tree... Done
Package freefont is not installed, so not removed

OK, I checked and Tahoma works fine for me. And if I
put it in my <alias><family>...</family><prefer></prefer>
it gets used as the default font for Arabic as well
as other languages.

So, no idea at all what is going wrong for you. Are
the glyphs you are seeing disconnected the right
ones for the Tahoma font?

Yes it works, It was a stupid mistake by me, I have only one
application which is suffering from this problem and that's what i was
testing.
It works fine with gedit & gaim.
Thanks for your efforts, and sorry for my stupidity.

Bug 110896 might be related to the problems you were
seeing with that one application.

No, have a look at the attached file.
If i include this file and remove thu 2 underscores "__" from the
variables, It cause the text to be disconnected.
That was the actual problem with the app.
perhaps it's another bug ;)

Created attachment 15783 [details]
header file.