You should definitely contact the support ninjas (1-800-315-OMNI or
omnifocus@omnigroup.com) and see if they've seen anything like this before. I haven't seen it myself, and haven't seen any reports of it on the forums, but that doesn't mean they haven't heard of it.
As a stopgap measure, why not add an action to each of these projects/SALs that you want to "protect" from this behavior, with a start date well in the future so that you don't see it? Then the projects won't really be empty and it won't matter if that checkbox is somehow changing state on you. You could also make yourself a project-mode perspective that just shows completed projects, grouped by completion date, closing all groups except for today and yesterday, which you could use to quickly check every day that you haven't completed any projects that you didn't intend to complete.