I've looked at it a bit and see similar issues, I think. I don't have a good answer. I did send a note to the development team, but might not expect anyone to see it until next week. You might try tech support (support link at bottom of this page).
Moving the script out of the project might be a solution; it seemed to work for my simple test.
Closing the linked tables in the project (so they don't automatically reopen when the project opens), then opening in some particular order might help. I had some conflicting results. It may be a timing issue more than an order issue.
Craige