I've got a project that has recently graduated from a TWR-K60F120M to the first prototype board, and for some reason I cannot get the USB to function properly on the new board. The prototype is using a slightly different MCU, specifically an MK60FN1M0VLQ15. The application is full-speed, host only. The USB works perfectly on the tower module; the attached tower.png image depicts a capture of an SOF frame. The next attachment, proto.png, shows an SOF from the prototype board. I believe the clocking is correct because, although distorted, the SOFs are being transmitted at the proper 1mS interval. In pursuing this problem, I've cut traces on the prototype board so the only thing attached to the DP and DM MCU pins are the two 33 ohm termination resistors, and that is what is shown in the scope capture.
In both traces, channel 1 is DP and channel 2 is DM.