Code that changes page numbering?

Hello, I’m an author who has used Scrivener 1 for windows for a couple of books. However one of my publishers claims to have a problem with word documents that have compiled from scrivener. In their words:

“For some reason, there is code in it that exports to Word, and causes the page numbering never to match up correctly from one computer to another.”

Has anyone else heard of this problem? Although I love Scrivener, I don’t want to keep having this problem.