And you downloaded a new copy of the Snapmarks template? Or did you just copy the marks from the first one you downloaded multiple times? (If that one is corrupted, they all are.)
If it’s not the marks or a particular file, you might have an issue with your machine that you need to tell Bonny about on the Introducing Snapmarks thread. That’s the only one they are currently monitoring for problems with the Snapmarks, and they need to know about them to fix them. (Vertical lines should come out vertical.)