Seems like I'm not alone.
So I start looking into this, first the back window seals, tailgate seals; the usual suspects. No dice. Then I find this after hosing down the top:
A closer look at my hardtop reveals holes:
Using a hose I confirmed this is where the water comes in and drips in the back area making it's way to the jack compartment. I also used canned air:
RTV to the rescue. Anyone else with these holes?