I am also getting the "permanent engine fairings" bug. I am using : B9, Chatterer, Distant Object Enhancement, DMagic Oribital Science, Environmental Visual Enhancements, Hotrockets, KAS, Kethane, Procedual Fairings, RCS Sounds and Lights, Scansat, Soundtrack Editor, Spaceplane Plus, TAC Fuel balancer, Mechjeb, Texture Replacer, Universal Storage, Active Texture Management and KSPRC.