Using CS6 (ME version) on OS X and when typing a full stop with Arabic keyboard selected, a percent sign in substituted. This happens on both existing documents and newly created documents. Font is Abobe Arabic and works with other text programmes.
Typing into other text fields with Arabic keyboard selected accurately inserts the full stop.
Same Here !
On Mac please go to InDesign>Preferences>Advanced Type and turn off "Use Native Digits When Typing in Arabic Scripts" option.