I've been having this same issue - the issue is quite reproducible for me, and it has been for years. I just finally grew tired of the issue and decided to investigate it, and yes, the issue is org-agenda-show-new-time.

I also have invisible entries in the org buffer, and the call to org-move-to-column apparently will move several lines forward, which causes us to process the same lines over and over.

Wrapping the call to org-move-to-column with a let setting the buffer-invisibility-spec to nil does fix the issue.

On Fri, Aug 23, 2013 at 8:08 AM Nick Dokos <ndokos@gmail.com> wrote:

Carsten Dominik <carsten.dominik@gmail.com> writes:

> I also do not expect negative consequences. Please apply the patch, will you?
>

OK - patch attached. NB: there is at least one place where the "wrap the
call to org-move-to-column" has been applied, in
org.el:`org-comment-or-uncomment-region', presumably for exactly this
reason. If this patch does not cause unexpected problem, then the
wrapped setting above can be cleaned up.

I hope it conforms to conventions but let me know of any problems.
--
Nick