My thinking is it is either getting checked too soon, or not unchecked soon enough, some sort of race condition. The scheduled script which processes it first is working through sublist items off of search results, having the box checked drops the parent record off the search though, so it processes the first sublist item and then doesn't process any more until the next execution. I'm switching my focus to trying to process all sublist items before checking the box. A colleague also suggested after I posted here, that the UI change may also be caused by a Client script being triggered when the record is saved dynamically