I just did another test with a different vc backend: the Mercurial
backend.
I created a local Mercurial repo and submitted a file that is not
completely rendered by vc-annotate with the SVN backend.
I modified the Mercurial hosted file, committing my changes in the
Mercurial repo.  Then I used vc-annotate on that Mercurial hosted file and
every line was annotated as it should be.

So it does seem to be specific to the SVN backend.


-- 
/Pierre