Those haddock warnings are annoying, but they don't cause any problems, AFAIK. I think the warnings were fixed in Cabal 1.18. I don't see them any more.
EDIT: OK, so we need to follow kosmikus's suggestion...
mv ~/.cabal ~/.cabal.SAVE
cabal update
This will create the file ~/.cabal/config. You can edit this file if you wish.
Now try building something and see if the problem is gone.