I may have been thinking of another vehicle for my earlier comment. I found a video on removing the fender flares from a gen3 tacoma (may or may not be the same on the gen4, and in turn the g6 4runner):
It has both screws on the underside, and snap-in retainer clips along the body panel interface. The odd thing is, in the video, it only looks like the orange clips snap in, and the ones between the orange ones (the area in question for your 4runner) are not.
Anyway, you've probably already tried this, but did you bump the fender flare with the heel of your had at the loose location, just in case there is a snap-in retainer clip there that just didn't engage at the factory? Or the clip may be broken. Either way, it's not right and should be covered under warranty.
PS, before you got the PPF, did you think the standard running boards did a pretty good job of preventing mud sling and pebbles (from the front wheel; I don't suppose they help for the back wheels) from hitting the door panels?