Hi Nicholas,
Thank you for the question!
I have a hunch that the merged file is using the wrong attributes inside the main file. Could you merge the "grey" file into a brand new file and see if the issue persists there. If yes, could you share with me the problematic file for further investigation? Let me know if you'll need a secure link to send the file!
Thank you very much!
Best regards,
Minh
Minh Nguyen
Technical Support Engineer
GRAPHISOFT