Just revisiting this to see if anyone else has a similar issue.

I only get water in the boot, under the spare tyre, if its really windy and wet. Never after washing the car or after just rain.

Eventually I caught the source and its coming in either around of from above the plastic vent flap in the back of the boot. Only on the drivers side. If you look inside the boot with the carpet up, right at the rear, as in just the other side of the bumper, you'll see a small vent with flaps on.

I have no idea how water is getting in here though. Possibly suction due to air pressure changes in the wind? Maybe its drawn in from the boot seal?