No, checkatleast doesn't affect which matches are returned (or at least
if it does, that's a bug).  What it does is provide a way to improve the
accuracy of the estimated number of matches (in exchange for doing a bit
more work).

The wording isn't very clear - I'll improve it.

If it helps, there are some tips for debugging why matches you expect to
see aren't found here: http://trac.xapian.org/wiki/FAQ/NoMatches