as in the title a leak into youre boot specifically in the little vents or near the arches? had a few people come to me the last week or so with this very complaint and i found the culprit first if you have a leak look under the rear headliner where it tucks under the boot rubber is it wet most likely it will be the rubber cover that protects the wires to the boot leaks if you notice where it sits ford designed a small hump to prevent water getting to this seal however if it rains heavy it does get to the seal and finds its way under from there it drips down onto the headliner and then runs down the wires all the way down to the corner of the arch. get enough in there it floods into the vents so people assume its coming through the vents when its not.

simple soloution seal it with exterior sealant actually pop the whole thing up apply the sealant and push it back into place smooth the sealant over and job done