I found it to be a long standing bug in libass.
To make the subtitles look right, you have to disable ass this way:
, set a font that supports arabic glyphs (Arial do), and codepage to CP1256 of course.
In the future maybe libass will correct the bug, until then fallback to plain osd.
Because the issue is very specific to few languages, i'd suggest you to file a bug to mplayer or libass developers so that they might correct the problem.