I have had issues with designing in arabic with my currect Indseign CC.
I then re-installed the the ME version of the software and it worked for a little while. But now it is reverting back to placing my arabic text running in the wrong direction.
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I didn't get it when you mention running in the wrong direction so I need to ask you some questions, do you have the Right-to-Left Type tool?
If yes and you've used it to create a text frame, did you use the Right-to-Left paragraph direction option found in the Paragraph panel? And had chosen one of the Adobe World Ready Composers?