Well, it seems that you missed the << ... >> stuff : you can't have a staff AFTER lyrics, but you can in parallel...
So you have to put << before the first \new Staff, and >> before the last }

May I suggest a clearer way to put your code (it is very insolent from me, but that's the way I managed to see where the bug was), such as :

(...)
musicI = {\key f \major \time 3/4
         \partial 4 c'8. c'16 |
         f'4 f'4 a'8. g'16 |
         g'4 g'4 bes'8. d''16 |
         c''4. \autoBeamOff a'8 \autoBeamOn bes'8 g'8 |
         f'2 \bar "|"

         \partial 4 c'8. c'16 |
         f'4 f'4 a'8. g'16 |
         g'4 g'4 bes'8. d''16 |
         c''4. \autoBeamOff a'8 \autoBeamOn bes'8 g'8 |
         f'2 \bar "|"

         \partial 4 a'8. bes'16 |
         c''4 a'4 c''8. c''16 |
         bes'4 g'4 bes'8. bes'16  |
         a'4 f'4 a'8. a'16 |
         g'2 \bar "|"
         }

musicII = {\key f \major \time 3/4
         \partial 4 s4 |}

words = \lyricmode {
        \set stanza = "1. "
        Ye who own the faith of Je- sus sing the won- ders that were done,
        When the love of God the Fath- er o'er our sin the vic- tory won,
        When He made the Vir- gin Ma- ry Moth- er of His On- ly Son.
        }



\score {
<<
         \new Staff {\new Voice = "upper" \musicI}
         \new Lyrics \lyricsto "upper" \words
         \new Staff = lower {\musicII}
>>
}

So the \score{...} part is really clear and the <<...>> quite obvious.

Best regards !

JMarc

On 15/09/2010 17:38, peterwinson1 wrote:
\score {
        \new Staff {
                \key f \major \time 3/4
                \new Voice { \voiceOne
                        \partial 4 c'8. c'16 |
                        f'4 f'4 a'8. g'16 |
                        g'4 g'4 bes'8. d''16 |
                        c''4. \autoBeamOff a'8 \autoBeamOn bes'8 g'8 |
                        f'2 \bar "|"
                        
                        \partial 4 c'8. c'16 |
                        f'4 f'4 a'8. g'16 |
                        g'4 g'4 bes'8. d''16 |
                        c''4. \autoBeamOff a'8 \autoBeamOn bes'8 g'8 |
                        f'2 \bar "|"
                        
                        \partial 4 a'8. bes'16 |
                        c''4 a'4 c''8. c''16 |
                        bes'4 g'4 bes'8. bes'16  |
                        a'4 f'4 a'8. a'16 |
                        g'2 \bar "|"  
                }
                
                \addlyrics {
                        \set stanza = "1. "
                        Ye who own the faith of Je- sus sing the won- ders that 
were done,
                        When the love of God the Fath- er o'er our sin the vic- 
tory won,
                        When He made the Vir- gin Ma- ry Moth- er of His On- ly 
Son.
                }
        }
        
                
        \new Staff {
        }
}
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