Comment #3 on issue 3160 by [email protected]: chord names pushed into the staff
http://code.google.com/p/lilypond/issues/detail?id=3160
The collision starts with the patch for 2148, commit 28f3294954eff1f263d3b2e3de1c520f4d2fbdfc
I cannot find which piece of that huge commit caused the change, but the change in behavior is that the lines of Lyrics containing "" now get empty skylines, where they did not before. This leads to issue 1669 for the Lyrics, because the line is empty in the sense of taking no space, but not in the sense of \removeEmptyStaves. The code I tried to remove in the patch for issue 1669 gets confused in this situation.
So the suggestion of issue 3156 seems reasonable: any line that takes no space would be removed in the sense of \removeEmptyStaves
