Prevent linux from clearing GPIO pins during boot

I have two GPIO pins that I’d like to be high during the boot process. These pins, GPIO 44 and 23, are connected to LEDs through some circuitry. I’ve managed to set those pins when uBoot runs, but they are reset during the boot process: as soon as the linux kernel starts these pins are pulled low. After linux finishes booting I install a device tree overlay and can resume control of the pins.

How can I prevent these pins from being cleared? Is this done by the linux kernel itself or some driver? How do I start looking for the code responsible?

(I also posted this question 3 days ago but it hasn’t appeared in the relevant group).

Some more information: I’m running the BeagleBone Black with a 3.8.13-bone33 kernel.

Adding the HWMOD_INIT_NO_RESET flag to gpio0 and gpio1 structs in
arch/arm/mach-omap2/omap_hwmod_33xx_data.c similar to [1] should work.