I'm quite sure we are talking about the same problem. Although perhaps I haven't been able to faithfully recreate it as you have.
What I have done is from the library I pressed all songs then pressed the shuffle all button.
Then I move to the player / album art screen. I tap on the album art to get the song list. Not really sure what that is. I select all then add them to the Queue. I do this in order to be able to prune out a few song I might not want to hear.
Unfortunately I cleared the part of the Queue I listened to from the first half of my shift in order to avoid scrolling down as much. I guarantee I listened to at least five cue generated tracks in my fist shift. Probably much more.
After the bug occurred while playing the Kinks I played a few "normal" single track files. Then another generated cue track. But it was the last track on the disk so I didn't notice it. Then some more normal tracks. Then It played a generated cue track perfectly.
So we seem to be having different experiences. But we are probably doing things differently. I've got 14585 lossless tracks in my library. If that matters. All different formats and whatnot.