@Joshua-Gans it's some subtle & rare thing indeed. My hunch is that it has to do with the particular point version of MacTeX installed together with the OS it was installed on, or on which it is running on right now. I wonder what happened if you cleaned MacTeX away and reinstalled it on the system where it doesn't presently work for you, as well as cleaned away the Manuscripts user defaults with
defaults delete com.manuscripts.Manuscripts (this clears away the information about the LaTeX installation path) as well as removing the
~/Library/Containers/com.manuscripts.PressRoom container directories (these contain cached data that can be safely removed).
The 1.0.30 which I can now definitely say will be made available tonight should help log at least some more info on the topic (it will not change the behaviour though).
@cerkut indeed, the pdftex binary has root as owner but read and execute rights. Is the result of the same file listing command the same for you as well, also for pdftex which pdflatex is a symlink to?
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