After doing some testing, I think this is a problem between KJR (possibly) and the auto strut feature. If I turned off auto strut on the fairings, the craft would fly normally and not be a stuck pendulum on the launch pad. In the Debug Console it will say "[Error]: It is illegal for a joint to connect to a rigid body to itself" Glad I'm not the only one having this issue, but like I said there is NOTHING wrong after I disable auto strut on the Procedural Fairing Base.
-Forgot to mention, when auto strut was on, and the craft was stuck on the launch pad like a pendulum as mentioned in a different post, I could eject the fairings and the craft would launch normally.