\version "2.11.39"
#(ly:set-option 'point-and-click #f)

\header { title="Cue notes mess up \voiceOne and \voiceTwo"}
\layout{ 
  ragged-right = ##t
}

vI = \relative c'' { c4 c c c | c c c c | c c c c | c c c c | c c c c | c c c c | c c c c | }
\addQuote vI \vI
vIIa = \relative c'' { e4 d f, e | \cueDuring "vI" #UP { R1 } | e'4 d f, e }
vIIb = \relative c'' { c4 b d, c | \cueDuring "vI" #UP { R1 } | c'4 b d, c }

<<
% after the cue notes, the voiceOne/Two settings are messed up:
\context Staff = "S1" <<
  \context Voice = vIIa { \voiceOne \vIIa }
  \context Voice = vIIb { \voiceTwo \vIIb }
>>
% killing the cues on one staff does not fix the problem:
\context Staff = "S2" <<
  \context Voice = vIIa { \voiceOne \killCues\vIIa }
  \context Voice = vIIb { \voiceTwo \vIIb }
>>
% killing the cues on both makes it work:
\context Staff = "S3" <<
  \context Voice = vIIa { \voiceOne \killCues\vIIa }
  \context Voice = vIIb { \voiceTwo \killCues\vIIb }
>>
>>