Twice now, my trunk is flooding from the rain.
It pools up in the middle and has rusted the Jack. and is ruining the interior back there.
No idea where it could be leaking from. =/ has this happened to anyone else?

 

First check the trunk lid seal to see if it is ripped anywhere...then look to see if the trunk lid is misaligned....

Could be around the window as well...

Don't you still have warranty?

 

Dan is right...

You could also be getting water entry via your Tail Light (s), IF the Gasket/Seal between the Body and Tail Light has shrunk or Tail Light Nuts are slightly loose you might be getting water in there.

If rust is on your Jack, then as Dan said check the Boot Lid Seal/Weatherstrip and or right rear Tail Light.

There is a slight possibility that your Trunk Lid Hinge on right side is leaking via a rust hole, or perhaps a loose Hinge Bracket Bolts.??

Also check the Body Filler Beading, that putty stuff between panel joins and then painted over, make sure the bead has not been damaged or broken by a slight nudged in a car park by another car, or cracked Tail Lamp Lens/Body done by another car.

Lift Trunk Lid and run some water around these 'dry'areas and see if you can pick up the water entry with a tissue paper.

 

Pull off the large back trim plastic that's across the back of the trunk and the two side formed pieces over the taillights. Look for any exposed holes or water marks. Water coming in there would logically go down into the tools/jack area.

 

^^All of the above^^
Also get a hose pipe and blast the trunk area. open the truck and see where the water is getting in.

 

Best way to find it is with help. Have someone hose the trunk area and you look through the center pass through with a flashlight. Look for water coming in.