I am using Poky linux for "imx31litekit", and it does not seem to detect CF cards. LoLo is accessing the cards perfectly.

The kernel is 2.6.19.2 and apparently has the right config options:
CONFIG_PCCARD=y
CONFIG_PCMCIA_DEBUG=y
CONFIG_PCMCIA=y
CONFIG_PCMCIA_LOAD_CIS=y
CONFIG_PCMCIA_PROBE=y
CONFIG_PCMCIA_MX31ADS=y

(Serial?) ATA is not enabled though:
# Serial ATA (prod) and Parallel ATA (experimental) drivers
# CONFIG_ATA is not set