Another thing to check is the outer cage pivot angle. FDs vary in effectiveness based on there the FD cage contacts the chain to derail it to a different chainring. When the rings were 52-42-30, the difference allowed the FD cage to probably contact the chain on the middle ring just barely and push it inside onto the small ring when down-shifting. But the 39t middle ring is now a tiny bit lower and so the cage isn't exerting as much inward push on the chain to derail it. You may need to carefully check the FD. If there is allowable clearance, lower it half to 1 mm down so it still clears the big ring, and if possible, loosen the clamp (if it's not a braze on) and pivot the FD clockwise a tiny bit when looking down the seat tube toward the BB. This should cause the cage to contact the chain just a bit sooner and with more force possibly to derail it properly. Test the up-shift to make sure that this doesn't harm the performance going the other way.