OK. I expected that rtl.css would be correctly loaded, because in this case, Polylang does use the option set when creating the language. With your previous setting, Polylang does not modify the setting chosen by WordPress.
I propose two different actions.
1. You can download the latest arabic translation of WordPress (which should correctly set the text direction) and upload the files in /wp-content/languages/
http://svn.automattic.com/wordpress-i18n/ar/tags/3.5.1/messages/
2. And / or you can download the development version of Polylang (1.0.3.3), as starting from now Polylang will always force the text direction based on the option chosen for the language.
http://downloads.wordpress.org/plugin/polylang.zip
the Arabic posts themselves are displaying in the English interface now.
How did you setup your theme translation?