This problem has already been fixed in the development version, 2.11.x.
If you want to stick to 2.10, see
http://lists.gnu.org/archive/html/lilypond-user/2005-01/msg00013.html
/Mats
John Rehwinkel wrote:
If I have an alternative with a note sticking out above the staff,
LilyPond moves the m
If I have an alternative with a note sticking out above the staff,
LilyPond moves the marker for that alternative up to avoid collision
(as it should). However, it doesn't move the marker for other alternatives,
which gives an uneven look.
\version "2.10.33"
\paper{ ragged-right=##t }
\relativ