I find that the rubber seal on the boot tray can cause the boot lid to not fully "seat" if the seal is dry. You can tell if this is the issue by removing the tray or removing the tray seal and see if your boot lid fully closes.
I put a very light smear of silicone grease on the outside of the seal which allows it to slide up into the boot lid and allow the lid to fully close. A bit of a nuisance as I'm always cleaning the grease off the boot lid as it attracts dirt.
