Hi Susan,
You have my attention because you're working with the Toolkit. It may or may not be related. I haven't heard of any integrity errors from it's use. From your post above, they are 'File' errors which implies a file structural problem, not an invalid customer or item. The next time you run the Toolkit, I'd recommend that you check your SA Data Integrity, before and after the Toolkit run. The Toolkit also generates a backup, so the 'Before' data is worth reviewing. The alternative is to stop using the Toolkit for awhile and see if the problem goes away.
Let me know how it goes,
Bob.