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?