> not at all, as you show way more input here as in the jpeg ... so first
> make a minimal example

I did gave a min-example, didn't I? The JPG was only to make clear, what 
I mean with "little signs". Is that clear now? Dont know how to say it 
better way (sorry my english) :),

> also "another font" is not revealing either
Of course it is not, yes, sorry. But sometimes I have problems with 
different fonts (e.g. the letters are not connected), and these problems 
do not occur in CorelDraw or some other programs. That is, what I meant. 
(Besides from that, it should be clear that I am a very big fan of 
ConTeXt and all the way I am talking about it to friends and collegues, 
so: no attacks at all :)).

> the only issue i see is that this otf font has 2048 units and gets
> scaled wrong (in luatex's backend probably)

The problem is not the scaling (may be too, but not my problem here). 
Don't you get the following problem in this (your) code?

\definefont[arabica][file:uthmantn1ver10.ttf*arabic at 45pt]
\definefont[arabicb][file:arabtype.ttf*arabic at 45pt]
\starttext
\setupalign[r2l]
\arabica شَدِيدٌۗ\blank\blank
\arabicb شَدِيدٌۗ\par
\stoptext

Maybe its an issue of my context-version, so see the attachment. With 
the font "arabtype" everything is fine, with the font "uthmantnver10" 
the sign is missing.

Huseyin