Upstream has an unreleased change making the test for mp4v2 more explicit for the older version: http://sourceforge.net/p/mediatomb/code/ci/bed8f03202336fc7863ec6a39e130473f59061c6/

The result of that upstream change is that it will no longer try to compile against mp4v2 and fail.

There is an outstanding patch in their tracker for updating support (via gentoo): http://sourceforge.net/p/mediatomb/patches/35/