Thanks Martin, this is not the problem.
Normally you can change the pinmuxing and GPIO configuration for every pin in a running Linux system just like explained here:
http://wiki.gumstix.org/index.php?title=GPIO
There's no need to go the long way of recomping your kernel or bootloader.
Either using the userspace gpio sysfs interface for exporting GPIOs or using devmem2 to set the corresponding PADCONF register directly.
If you only want to change the pinmuxing mode you can also use this very handy kernel-driver (https://github.com/ftagius/OMAP-cmpc) which also exposes a userspace interface to /dev/cmpc to set pinmuxing, e.g. setting GPIO186 to pinmuxing mode 4 (GPIO mode)
$ echo 186:4 > /dev/cmpc
cmpc: 0x480021e2  PIN 186 (0x0114) : IEN | PTU | DIS | M4
cmpc: 0x49058034  GPIO_OE[5] : 0xFF7FFEEF bit 26 is ON (input)

Cheers
Phil



-------- Original Message --------
Subject: Re: [Gumstix-users] Change pinmuxing for GPIOs 127 & 128 in Linux won't work
From: Martin Stoilov <martin@rpasearch.com>
To: gumstix-users@lists.sourceforge.net
Date: 02/14/2013 08:23 PM
I had to change the muxing for GPIO 144, 145 in one of my boards. I did
omap_mux_init_gpio(144, OMAP_PIN_OUTPUT);
omap_mux_init_gpio(145, OMAP_PIN_OUTPUT);
in the board initialization function and it worked fine.

-Martin