The winalign within SDL Studio 2011 offers a limited set of languages and unfortunately does not include the two languages that I work in - Pashto and Dari! There may be other languages as well that are not in the list.
No experience with WinAlign, but here is a generic workaround you may want to try: pretend Pashto/Dari is a similar, supported language and see whether you get a usable alignment. If so, export the TM you obtained to TMX, change the language code to that of Pashto/Dari and import back into Studio.
An alternative would be to use LF Aligner, which supports Pashto and Persian (maybe that would do as a temporary substitute to Dari):
LF Aligner is very good and it's free.
Is there anyway to add a language to the list of target or source languages?
I would be very surprised if it were possible.