I intermittently get the same problem on a Beagle-xM running the latest code 
from inux-linaro-2.6.38.git
I have the .config from the Alpha3 hardware pack but with Thumb2 enabled. In 
this, config. CONFIG_I2C_OMAP and CONFIG_GPIO_TWL4030 are 'y'.

For a successful boot, no modules are loaded before the rootfs is
mounted on the MMC. After boot, lsmod gives

Module                  Size  Used by
smsc95xx               10589  0 
usbnet                 14739  1 smsc95xx
omap_wdt                3653  0 
omap2_mcspi             6611  0 
twl4030_usb             4117  0 
twl4030_pwrbutton       1302  0 
gpio_keys               5328  0 
leds_gpio               1954  0 

I tried turning on some debug macros to see if I got anything
interesting and now found I can't reproduce the problem with or without
the debugging. It's always the way :-(

There are several warnings and errors during boot which are probably not
be relevant - they seem to be another bug which is fixed in Ubuntu
2.6.35 kernels
(https://bugs.launchpad.net/ubuntu/maverick/+source/linux/+bug/607250)

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https://bugs.launchpad.net/bugs/712175

Title:
  OMAP Beagle C4: kernel does not reliably find SD card on boot

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