Although this thread seems to be stone-dead, I'll just try my best to rehash it...
I recently have just the same problem as Frannz. Plugged the CF into a card reader, connected my X5L via USB and moved the content of my 30 GB Toshiba drive (MK3006GAL, 50 pin) to a brand new 128 GB 600x CF (KomputerBay). Then I installed the current bootloader (I think it's version 4) on my X5L using RockboxUtility 1.4.0, unplugged the USB, plugged in the AC and booted up the X5L to finally install the bootloader.
I also installed the current Rockbox (3.13) on the CF via RockboxUtility 1.4.0 while still plugged into the card reader.
The CF card then changed its home from the card reader to a CF adapter ("M-ware® ST5051 CF an HDD-Adapter ID7595"). Finally I swapped the Toshiba drive with the CF adapter.
Whenever I try to boot my X5L it shows "ATA error -32". I had tried before without upgrading the bootloader and Rockbox - previously installed were the dual boot loader and Rockbox 2008-02-12 - and it showed "ATA error -31".
What am I missing? The CF card is formatted to FAT32 by factory, has one partition (active, primary, Windows stating 120.24 GB). Do I have to make the partition bootable? Is Rockbox capable of this size of CF? Maybe the CF adapter is broken?
Thanks for any help!
Cheers
Oliver