Hi Ian,
For this specific case a posted file would be helpful.
There are some things you can try to play around with to see if it gives you the transcription you want.
In Setup/Transcription Options:
- check the "Remove Overlaps of Notes" option.
- under "Remove Rests Smaller Than..." check the "Do Not Remove Rests".
- under "Transcribe Ornaments", check "Grace notes."
- near the bottom, check the box for "Two-notes chords in a staff that has mostly solo notes should be sequenced as two separated notes."
If those don't help, you can then try using Format/Convert to solo notes, and select the staves that you want to use the command on.
If those don't help, please do post the file or a part of it for us to take a look at it.
ttfn,
Sherry