What am I doing wrong???

[Michiel Lange]

Hello, my name is Michiel and I will admit first that I am very new to 
lilypond.
The examples shown look great, so I was about to give it a shot... the 
first few lines of music went well, so I felt ready to put my first 
piece of music I ever wrote into lilypond.

It's a piece for organ and the following should be the first two 
measures of the piece, but somehow the bass and pedal "shift" to 
respectively the third and the fifth measure... Anyone who can tell me 
what makes this happen?

\score
{
       \notes\context PianoStaff <<
       {

               \context Staff
               { \relative c'
                       {
                               \key d \major \clef violin
                               r1        r2    r4   <<fis4 a>>
                       }
               }
               \new Staff
               { \relative c'
                       {
                               \key d \major \clef bass
                               a2  fis   d4  e4  fis2
                       }
               }
               \new Staff
               { \relative c
                       {
                               \key d \major \clef bass
                               a2 fis2 d4 e4 fis2
                       }
               }
       } >>
}

(I also use to be a C programmer, and use this style of coding for 
readabilty for myself, as I often forget a brace here and there...)