My 2006 will do the same thing. PopUp Gizmos will help but not eliminate the problem. I gave up and just fold up a small towel in the corner and change it out frequently.
On mine it seems to follow the channel where the canvas attaches and then exits the bottom.
2006 23B Hybrid with 10k round bar WDH
2011 F150 4x4 SCREW Ecoboost, Max Tow, Integrated TBC, 3.73 LS axle, Firestone Ride Rite airbags.