Happened to me just now, Skim 1.7.17 (169), macOS 27.0.1.
I had the following setup:
Ctrl + Cmd + P.Cmd + W.Interestingly, though, after Cmd + W I was still able to view the closed PDF in the presentation mode.
I would expect Skim to leave the presentation mode after closing the PDF with Cmd + W.
(I'm not sure what happened exactly, I panicked a little and started spamming Cmd + W/Cmd + Q; I ended up with shutting down my computer via a keyboard shortcut).
I cannot reproduce this. For me, Cmd-W does nothing (well, it beeps) when in presentation mode, as borderless windows should not be closable. So somehow Apple has introduced a bug when attempting to close a borderless window. Also I don't see how the tabs make any difference, as a presentation window is never in a tab (it is removed from the tab before going into presentation). Are you sure this is relevant?
I cannot reproduce this. For me, Cmd-W does nothing (well, it beeps) when in presentation mode, as borderless windows should not be closable. So somehow Apple has introduced a bug when attempting to close a borderless window. Also I don't see how the tabs make any difference, as a presentation window is never in a tab (it is removed from the tab before going into presentation). Are you sure this is relevant?
I have reimplemented closing a document in presentation to simply ending the presentation. This should prevent pathologies to occur.