After doing some edits and typing Cmd-S, the file saves but the black dot in the red close button, indicating a dirty file, remains after the save operation. Saving a second time clears the black dot.
It’s working fine for me, although sometimes it does take a little longer to save, especially if it’s a big file. In the Version History, p. 85, Daniel mentions that thumbnail pdfs are created by default every time you save, to be used in the future for Quick Look support.
You can turn this off in File → Project Info. I have a big project I’m working on now, and turning this off made saving faster.
Thanks, Stephen. Turning that off in File → Project Info did the trick. It now saves way faster and the black dot clears immediately.