Yes, Lilypond wastes 10% of the vertical space on each page. You
have 98 left,
but lilypond reserves a little less than 20 units for possible
rounding
errors when calculating the staff spacings (yes, I agree, that's
insane!). So
lilypond thinks there is only ~80 staff spaces left, while the
second system
needs 90.
This came up a while ago on the -devel list:
http://lists.gnu.org/archive/html/lilypond-user/2008-06/msg00145.html
http://lists.gnu.org/archive/html/lilypond-user/2008-06/msg00329.html
You might try to comment out (or at least reduce) these 10% of
reserved space
and see if you run into any staff collisions (which I don't think
should
happen, but then I haven't dug deep enought for this staff!).