Sorry, I didn't know that now you are working on Persian language on non-Persian wikis, Is this done by an extension? It is great (and far more better than commonswiki's localization)
I am fixing a lot of bugs of RTL languages. More improvements coming soon. I aim the site here to be nearly perfect :) And it will be in the software by default soon, and it will reach Commons and other wikis by the end of this year or the start of next year. So if you have feedback or bugs, please say! (Btw, I will look at the issue you said, when I have time.)
First thing that I can see somewhere in mediawiki UI (same #p-views > ul and #p-personal > ul) have lang="fa" dir="rtl" but #mw-panel have not, also #mw-clearyourcache (on this page) have not lang="fa". It is a minor problem but can you see what happened?
I fixed the reply count in mwr:91528.
As for the lang="fa" dir="rtl" attributes, I can add it, but is it needed? Are there problems with it?