I'm sorry - I'd need to see the CSS you used, and what you think is displaying incorrectly, to draw any kind of conclusion.
I saw
Doitsu's response in your Sigil thread about RTL css. Is this something different?
I have to admit that it has been many moons since I studied Arabic in college, but it appeared the word order was not consistent in the image in his post. Is that the issue? I attributed the word order thing to my not being familiar with different language keyboard procedures - I completely defer to Doitsu's expertise there.