Which ULPI registers are written (and what are the values) when USBHS_PORTSC1.PHCD is set or cleared? I am trying to disable all pulls on Dp/Dm pins as I think they are messing up charger detection on our battery charger. I set the bits in the ULPI transceiver, but after clearing PHCD, the bits that I set are no longer what I set them to (in this case, I wanted to set the opmode to non-driving so that the transceiver tri-states drivers).
Have you checked the datasheet of the ULPI interface IC? In case of the USB3300 chip included on the TWR-SER2 board, it has the capability of enabling/disabling the internal pull-up/pull-down on both D+ and D- pins. Regarding the software, you could refer to the examples for TWR-K60F120M and TWR-K70F120M boards from Freescale USB Stack v4.1.1 or MQX v4.0.2.
Hope this will be useful for you.