One application "failed to quit" on auto shutdown

This has been happening daily now for perhaps a month, and it's got me stumped. I can't identify any pattern or anything.
I have my system scheduled to shutdown overnight and start up in the morning, and have had this same setting for years. What's happening lately is that the unattended shutdown apparently times out and I get a message saying logout failed "because the application [X] failed to quit." Now the really weird bits -
'X' is almost literally a different application every day, and it's rarely if ever attributable to an unsaved document. I think it's happened at least once with every single one of the applications I regularly have running. Sometimes it's an application I've used in the course of the day, and other times it's one I haven't touched. But it happens every day.
if I manually select the shutdown menu command at any time, including after finding that the auto shutdown has again failed, the shutdown runs smoothly with no application failing to quit.
I've run 'repair disk' in Disk Utility and also Disk Warrior and applejack several times each, as well as a weekly scheduled batch of maintenance tasks (using Cocktail). None of these operations has changed the behaviour come shutdown time.
Has anyone else seen this?  Solutions anyone?  Thanks.

I'm 'bumping' this one.
Still happening very consistently, and becoming a real problem. Since originally posting I've run all the disk operations many times over, as well as one or two system updates at least. Nothing has changed, it just happens like this every night.
The only thing I can offer as a (sort of) pattern is that the application that's most often the one reported as preventing logout is HistoryHound. And it would appear to be one of the first ones the system tries to quit in its shutdown, since most of the apps are still running. However it does still vary - it happens on a different app sometimes, and it happens on some app when HH wasn't even running. So not sure that's much of a clue - unless perhaps certain apps are taking longer to quit than the system expects (or something??? - scratching for clues here ...... )
Can anyone help? Please ....

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