Those are inductors/coils in the picture you red circled.
Not sure How you measure short, if you probe one side to other, then yes, it is short by definition of inductor/coil. Or if you put one probe to ground, another probe to on side of the inductor, that is the proper way of measuring SHORT to GROUND.
Since you mentioned working normal in handheld mode. There should not be the problem or you wont get device boot up.
Back to the original topic, not sure if you have breakout board to insure all pin from new port(especially hidden lines) got seat properly