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That checkbox should only change state on user command. Do you have the default for new projects to be completed automatically? I also make extensive use of SALs, but have not seen this behavior. One likely difference is that I do not autocomplete new projects by default. I do not know if that is significant.

As a safety measure, you could add a dummy action with a start date far in the future to any SAL where auto completion is unwelcome.

Do you use OmniFocus syncing?

Whenever this bug happens, you should immediately contact Omni support. It may be possible to find a clue as to why this happens by looking at the transaction history in your database. That history may not linger for long, so don't delay once you notice it has happened again.