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Sorry for the trouble, Chris - when OmniFocus is deciding whether something should appear in one of the date-based filters, it looks at the item itself, but it also looks at any rows that item descends from.

Example: imagine a project whose due date is set to Tuesday, while one of the rows in the project has the due date set to Friday. Both rows will appear in the Due Soon perspective on Monday - when there's a conflict, we figure it's better to show you something too soon than too late.

That's usually what causes situations like you seem to be describing - a parent row has an earlier due date set than the rows that "shouldn't" be appearing there. If that doesn't sort everything out, though, email some screenshots of the offending items to our support ninjas and we'll be happy to investigate this with you.