Ah - ok - yes, I understand that - worth trying

It is a single chorus song - (actually, I cant remember about that example I posted - but the actual one that I was having the problem is is just one long arrangement - no repeat chorus)

So, I just repeated the simple exercise to be sure

1) New track Key of C - no transposition
2) Set 1 chorus 12 bars
3) first 4 bars C, with 'walking chord progression in melody line C E G C
4) Bar 5 - Edit> Settings for bar to D - enter Chord of D, enter walking chord progression in melody line for bar 5 as D F# A, D
5) Bar 9 - Edit > Settings for bar to E - enter chord of E, enter walking chord progression in melody line for bar 9 as E, G#, B, E

This plays OK & looks ok in both notation & full page view - the key signatures all show at the correct bar positions, etc

6) set 'opt' dialog and set transposition to '2' (Tenor Sax Bb)

Bars 1 - 4 show 2 sharps (D) - Chord & melody line has transposed to DMaj (D F# A D)
Bars 5 - 8 show 2 sharps (D) - Chord has transposed to E - melody line transposes to use EMaj but are shown with the G# as an accidental
Bars 9 to 12 - show 4 sharps (E) - chord has transposed to F# - melody line transposes to F#Maj but shows A# as an accidental

If I now attempt to enter new notes - I have to remember to add accidentals to fit - this explains my original problem - I had assumed that key signatures would work this all out.

So - this still has the same problem - I think there is a bug when applying transpositions and key signature changes ... Pity that my melody line is transposed....