Hi Adam,
Please construct a minimal example. Do you need all those \overrides?
Do you need the manual beaming? The multiple staves? By "minimal", I
mean "anything that can be gotten rid of, while still demonstrating the
bug". There are more hints here:
http://lilypond.org/web/devel/parti
> I'm not top posting.
%% Full measure rests are not compressing along with music passed to the
%% compressMusic function. Note that replacing "\time 3/8" with "\time 1/6"
%% in the second staff of the example below sidesteps the problem.
\version "2.11.33"
\paper {
ragged-rig