Ref branch 1.1-master:
The scheme for padding (and multi-row-align?) puts every character in it's own span. On webkit based browsers, this causes the arabic character formation to be broken.

in the attached Arabitest.ttml sample, the characters should join, i.e.

should look like:

or even like

(the third image is from iexplore)

personally, I think the third display will be too difficult to achieve consistently across all browsers and renderers, and would be happy to caveat joining character sets in the standard to indicate that characters in different spans will specifically NOT join (but we may then need to MAKE them not join in iexplore). Especially as they do not join in iexplore if styling is more different than just color?

Arabictest.zip