I’m curious how this happened (Dorico Pro 4.0.31), the orange notes shown. I had written them in the wrong voices, so the stems were flipped the other direction, and Dorico shifted the noteheads to fit correctly. When I swapped the voice contents, they remained shifted as shown, with nothing in Properties turned on.
I could use Engrave to fix this, but hoped Dorico would have displayed these correctly, and wonder if I did something wrong.
Edit to add: Attached are just the notes in question, copied and pasted into a new flow. They do the same vertical misalighment. Vertical_alignment.dorico (417.0 KB)
In addition to what Dan has stated regarding voice indexing. What is going on with your voices? You seem to have three voices where two would do as in the attached example:
@tbabcock123, you may be misinterpreting the orange notes in the picture. I had selected them, thus they turned orange. I’m just using two voices.
@dan_kreider, your advice was spot-on, thanks. I’m not sure why either. I also don’t know why I didn’t notice, as I checked the Properties! Maybe I need new glasses.
(Just for completeness, notes/rests/items can appear grey in a number of circumstances: because they’re implicit rests, have suppressed playback, are in a unison range around a divisi change, are in a cue, are on a condensed staff)