Is this a project that has been freshly upgraded?
Red squares are seldom good news. Most often, they indicate an output file has ended up back in the project and is being used as a source file.
Can you share a screen shot of the HTML view of one such file? Doesn't matter if you have removed the squares or not. I'd like to see the HTML code at the top of the file.
If I can remember one of the many, I'll send you a screenshot (there were hundreds of them, not all in sequence).