I use Arabxetex and Polyglossia from Texlive 2013 on an OpenSuse 13.1 system to write Arabic. The Arabic text needs to be fully vocalized.
There are no Problems writing unvocalized Text, but adding a vocal sign breaks the connection between consonants: the words come out as a series of disjointed Arabic letters in their isolated letter form.
Has anyone else had similar problems? I don't know how to solve the problem.