UPDATE: Okay so to be sure, I downloaded the stand alone add-on manager and also GSX, reinstalled, it asked me to update the AFCAD files, so I say yes, and then i had to reactivate SODE. After this I fired up PHLI again with the mytraffic PHLI bgl on as by default, saw the double markings, so I quit P3D, went ahead and disabled that file, then loaded up P3D again, double lines are gone, but the problem is still there when I go ahead and access the GSX menu, it gives me a green bar along the top with a message saying:
[GSX] System error while trying to access E:\Applications\Mytraffic Proffesional\mytraffic\scenery\BR2_PHLI.bgl Createfile failed, the system cannot find the file specified ... (system: 2)