Transpose dialog can lead to transposition errors/inconsistencies in parts
In some cases transposition by key, can lead to errors in parts.
The error can be regularly reproduced with the attached file.
1) "select all".
2) From the menu bar, choose Tools → Transpose….
3) Tick "Transpose Chromatically" and "To key".
4) Tick "Transpose key signature" and "Transpose chord symbols" (leave as is)
5) Tick "Closest", and select a destination key signature (e.g. G).
6) Click OK.
The whole score is transposed correctly, but the Organ part has lots of errors in measures 7 and 8.