OK, no problem. Since this is resolved on your end, i did not verify the simple fix of just disabling ADSP using systemd, but the what did work in the past was disabling the ADSP using systemd AND makding the device tree change I mentioned above.
Just to clarify what is happening, the GPIO can be accessed from CPU and other sub devices in the SoC and in this case if ADSP is enabled, once ADSP starts up, it configures those pins for some audio clock/data functionality and CPU loses control over them. The behavior is such that during the system boot, the CPU initially (first few seconds) seems to have control over the pins, but then ADSP starts up and takes over, and it even sends some clock/data on these pins (a short burst). Therefore, disabling ADSP allows CPU to maintain control over these GPIO pins.