Transpose with Multiple Keys

I have been using Windows 0.9.4 R1598 (and 0.9.5 R1897)

I have a 123 bar 5 voice score.

Bars 0-52 have a key signature of D major

Bars 53-65 have no key signature - (well C major)

Bars 66 to 93 have a key signature of E major

Bars 94 to 123 have a key signature of D major

I have a double bar between different signatures. The score was originally created in D major. I dropped a key signature in the measure when I want to change the following measures.

I wish to transpose the whole score by 2 semitones

With 0.9.4 I select all, go to transpose, select -2 semitones and check transpose key signatures I get the following as key signatures

0-54 C major (two measures past the original D end) (from original D major)

55-65 B flat major (from original C major)

66 A major (original key signature A major)

67-93 D major

94 -123 C major

Why would 66 not change key signature- the notes changed

Why would would it go past 52 and put an additional 2 measures as C major when then should have gone to B flat

Any suggestions on how I can get achieved what I wants 2 semitones over the whole score?

Thanks

keith