Hm, I could have sworn I tested it with 'emacs -q', but apparently I made a mistake. In the end, however, it boiled down to corrupted part of '.emacs' where customization variables are (this is an alignment rule):

     (open-comment
      (regexp lambda
              (end reverse)
              (funcall
               (if reverse
                   (quote re-search-backward)
                 (quote re-search-forward))
               (concat "[^
\\\\]"
                       (regexp-quote comment-start)
                       "\$.+\$$")
               end t))
      (modes . align-open-comment-modes))

The string after 'concat' looks very incorrect and when I replaced it with the proper one from current source code, comment eating is gone. Of course, I cannot guarantee I didn't modify it, but _maybe_ at some point Emacs screwed it up itself. Can you try customizing 'align-rules-list' in a harmless way and check that what is written in Elisp is actually correct?

Paul