Hi Ravage... I'll give you my best guess. Our GT's - like many modern cars utilizes serpentine belts and this is what is employed for the SC. Our car have a tensioning arm and the purpose of this arm is to keep a constant tension on this belt as the engine accelerates and decelerates. These tensioners have a finite range of motion as well as a midpoint. It is pretty amazing to watch a GT engine run and rev and to see just how much this tensioner arm moves around. By design, when you have an OEM SC with an OEM pulley, these tensioners are set right at their midpoint of motion. When you make what is seemingly a small change - like a smaller pulley for more boost (one of the most common GT upgrades), now the belt is fractionally to long and this tensioner in no longer at its midpoint and so the range of motion has been compromised. Many of the Pulley/Tune upgrade kits simply ignore this but the Ford Racing pulley/tune upgrade kit includes spacers for the power steering pump. By scooting the power steering pump over a smidge, they are able to compensate for the smaller pulley. Ford takes this extra step to insure the tensioner is at its midpoint. (Interestingly, some installers simply discard these spacers as it is one of the more time-consuming parts of a pulley/tune install - and presumably they know better than Ford... but that's a story for another day.)
As has been stated by myself and others, the belt length that Whipple recommends is (or maybe more accurately, historically wasn't) available in the proper length. So, Whipple was buying the proper length 12-rib belt and cutting it down to a 10-rib belt - hence the premium cost. Now, you state that you are sourcing an 10-rib belt directly. So, either 10-rib belts are now being made in the proper length or you are buying a belt that is the wrong length for your application.... which could be all or part of your problem.