Kurt, honestly, we have no kernel components. When we're not running, we're not running. We don't interact with the system in any unusual way. The schedules are fired with either cron or launchd, in an entirely standard manner, and you can even look at the schedule drivers, since we supply them in source form. They're written in Applescript. Applescript can't cause your system to hang on shutdown either.
So, something else is clearly going on.
What happens if you start up in Safe Boot, then set a schedule to run a few minutes from "now", then shut down?
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--Dave Nanian
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