Publish rules at Org level and Product level causing drawings to publish with incorrect line colors

We have publishing rules in place at organisation level to control what gets published based on EPMDoc name, everything is working as expected. Today we needed to put a specific rule into a product folder and now when drawings in that folder publish they publish with Creo line colours instead of monochrome. After some investigation it seems like if we put any rule in any folder while also having a rule at organisation level, the drawing will not publish in the correct colours.

Worker logs show that it still uses the correct recipe file, so I thought perhaps its not using the pentables?

Has anyone experienced a problem like this, my only work around is to edit the organisation level rule to capture the unique naming convestion, which means re-writing almost half of it and validating all conditions again, which I would rather avoid.

Thanks in advance!