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To quote that pointy-eared chap: "fascinating" :-)

I just installed the latest sneaky peek after examining that checkbox for all 40 of my SALs. Count of SALs with checkbox set

before update: 0
after update: 0

How do you have the preference set for auto-completion ("When completing the last item: [] Mark the project or group complete") at the bottom of the Data preferences pane?

I just discovered that if I switch back and forth between OmniFocus 1.6.1 and a more recent version, that checkbox gets enabled on a SAL if and only if I had the default set to auto-completion.