My computer just self-upgraded from Skim 73 to 74 and immediately quit saving the notes that I made on files. I would read my article, make highlights and boxes and whatnot, save the document several times throughout the process, check to make sure the notes were in the note pane before I closed, and then close the window. I then reopened the window to review my work and all the notes were gone. This has happened with two articles tonight, since the upgrade happened, losing hours of my work.
Equipment: MacBookPro, 10.8.2.