Well, if you have evidence of the tire hitting, then I would agree that you have a clearance issue. Whether it's a suspension issue or the result of larger tires that have been installed, perhaps when you went to an "F" rated tire, remains to be seen.
It could be that the springs are not strong enough to support the weight of the trailer. Are they flat, or are they very nicely arched? Some of the builders are notorious for putting just enough suspension to get the trailer to the dealer. You may need to upgrade your springs.