Found a bug with embedded cuesheets.
I have a flac that doesn't have an embedded cuesheet and a separate .cue.
After using right click -> utils -> edit cuesheet -> load from file
all the tracks are messed up.
The order of the tracks has changed.
As far as I figured out that's because that single flac image had its own track number (e.g. 1).
So before embedding the cue sheet I cleared up the track number field and now the order is OK.