This is not an exact solution to your syntax highlighting issue but
rather a solid way to debug VIM issues. Please don't mark this as the
solution to your question.
I would manually go through your ~/.vim/bundles/ folder and
mv each plugin out one by one until you find the culprit.
Start with the plugins that are likely to be causing the problem and
continue from there. I.e, vim-markdown is more likely to be causing these issues
wap-it (my VIM plugin ;) ).
If you still haven't found the culprit after moving all your plugins
out, I would then ensure that you're running the latest version of VIM. If
THAT doesn't work, I personally would try reinstalling but I'm also not
very well versed regarding VIM's internals.
Hope this helps,