Weird input behaviour with PINMUX_GPIO

**Describe the bug**
I use the `rc_pinmux_set()` to set some of the SPI pins to regular GPIO as well as using it for some of the normal GPIO pins as well to set pull-ups. Now the strange thing is that if I chose either `PINMUX_GPIO_PU` or `PINMUX_GPIO_PD` as the mode there is no problem, everything works as expected when I read the inputs. But if I chose `PINMUX_GPIO` then some of the pins are stuck to only reading 0.

I am using *GPIO1_25, GPIO1_17, GPIO3_20, GPIO3_17, SPI1_MOSI, SPI1_MISO, SPI1_SCK, SPI1_SS2* and out of those *SPI1_MOSI, GPIO1_17, GPIO3_17* are not reading anything but 0 unless I activate the internal pull-ups/downs.

**To Reproduce**
Set the before mentioned pins to `PINMUX_GPIO` as well as initialize them as input using `rc_gpio_init()`, if you read them they only return a 0. If you instead enable pull-ups/downs with the pinmux, then they work as expected.

Start by reproducing the behavior with rc_pinmux_set() and rc_gpio_init() on the listed SPI and GPIO pins, comparing PINMUX_GPIO with PINMUX_GPIO_PU and PINMUX_GPIO_PD. Trace the pinmux and GPIO input paths to determine why the affected pins read only 0 without pulls; done means the affected inputs read correctly in the plain GPIO mode and the behavior is covered by an appropriate validation.

Written by the indexing model from the issue text.