May have found problem
I may have found the problem. The pages I seem to be having trouble on are the pages that have an include file with a form at the top of the page (a search field and button for instance). When I create/edit a form in the main file (not the include), Validation Toolkit gets messed up. I have tried this on several sites, and this happens every time. When I run Validation toolkit on a plain Jane page with no includes, it is fine.