In arabic locales national characters are disjoined in jEdit. Tested on both sparc and x86 under ar_SA.UTF-8 and ar_EG.UTF-8 locales on Nevada build 94.
It looks like a problem of jEdit only. In other applications characters are connected properly. Even in jEdit, but in the main editor characters are not connected. See the attached screenshot.
You can download jedit from www.jedit.org