Running the existing release alongside a potential new release is a great sanity check to make sure that any new changes haven't had any undesirable effects on the results.
Today this happened (the new Integrity Pro and existing release are showing different results):
The reason is that I'd put some A/B testing in place, there are a bunch of pages with differences and A or B in the querystring. It's in an area of the site I'd normally ignore for reasons, but didn't today.
Therefore, the list of pages may feature both the A version and the B version (because the url of the page is the unique key for Integrity). So those pages may be duplicated in the results, or maybe not, and that's a matter of chance.
Ignoring querystrings fixed the problem, and now gives consistent results every time. (Querystrings aren't used for any other reason on this site, so it's fine to ignore them).