Thanks for the reply Johnny. Yes, it did work when I changed the password in Site A and then synced. Dirsync in general is running fine and it seems to just be password changes made from domain controllers in Site B. I've got my network guys looking at the AD structure so hopefully we'll find a reason for the issue. The first question they asked me was should this work with two sites but you're indicating it should so that tells us something there.
Thanks,
Angela