@Spooniest
What I meant is, let's look at the progression:
A B C# B A G# A B A G# F# G# A G# F# F F# G# F# F
F# G# A G# F# E F# G# F# E D E F# E D C# D# F D C#
F#--------------- E---------------- D---------------- C#---------------
I put the part in bold, in the last section the middle voice uses D# (the major second of the C# major scale, as expected) when moving up but D (minor second) when moving down. When the "synth line" kicks in, this quirk disappears because this voice is now used for the synth line.