.
The Mishafi font from Diwan:
http://www.diwan.com/mishafi/main.htm

...has over 3000 glyphs and is designed for correct display of
the Quran.  Presently, it is only correctly supported by Diwan's
software applications.  This suggests that your question about
the issue could be answered that it may be both a font issue and
an operating system issue, as well as an encoding issue like
Yung-Fong Tang has pointed out.

There are many fine Arabic script font developers working
on OpenType Arabic fonts now, and we should see an increase
in the number and quality of Arabic OpenType fonts in the
future.

Meanwhile, one approach could be to continue using the
existing graphic format in order to provide proper and
elegant display while adding plain text Arabic to each
graphic page so that searching and indexing will work.

U+0644-U+0623         gives your figure 3 on this system
U+0644-U+0654-U+0627  breaks ligation
U+0644-U+0627-U+0654  gives ligature but no hamza

Still, I think Yung-Fong Tang is right about using U+0654 instead
of U+0621.

Best regards,

James Kass
.

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