I am also having the same problem with our company newsletter. Not only do the links not take you to the correct section, you have to double click the originating links to the anchor points before they will work at all.
Come on Apple, how about a response to this thread?
I am also experiencing this issue with an HTML mailing, and have reported it to the URL above. If you're having the same problem, please report it too...Apple only fixes these things when enough people complain.