I've patched the kernel to set a certain GPIO to LOW. It works well after the kernel boots and the OS is running.
However, when powered up, before the kernel is loaded, all GPIOs appeared to be set HIGH. This causes all devices I connect to these GPIOs to turn on for a few seconds, just before the kernel is loaded.

Is there any way to set these GPIO to LOW by default?

Need to patch bootloader too

Where can I get the bootloader source code to patch?

I noticed that the carambola board I purchased earlier in the year does not put GPIO12 and GPIO13 (UART1 DCD, UART1 DSR) on HIGH, but all 8 boards I purchased lately does.

Could this be because there were changes to uboot from the earlier version?

After more testing, I can confirm that those boards with the older bootloader does not set GPIO12 and GPIO13 to HIGH. Only those with later bootloader do. I think the later bootloader, which added firmware serial loading, sets the UART1 GPIOs to output, which explains these GPIOs to go HIGH before the kernel loads.

I think what we simply need is the old bootloader to flash to our boards, no need to patch and build new one. Do you still have the old bootloader for download?

I have the same problem on newer modules.
Deactivated ttyS0 GPIOs (we use RX/TX and n o t active signals like CTS...)
go up to 1 on boot and back to 0 when kernel starts.

Checked against older modules and verified via mmio/io to
have 0x1D on GPIO purpose select all set to normal GPIO.

Any new infos ?
Bootloader downgrade needed?