I've had a series of CF corruption problems when transferring files to and from OSX 10.3.9. In particular, the latest firmware update allows the iLiad to export its CF card through its USB port as a USB drive, and though this works fine on Linux (Ubuntu) and WinXP, when I tried it on OSX I corrupted the card to the point that I nearly had to scrub it and start over. I eventually was able to repair the filesystem on WinXP, but not until I removed the card from the iLiad and used a separate adapter. So be careful with CF cards and OSX. I think it's an OSX problem, actually -- I think the OS isn't correctly unmounting the virtual drive. (I think this because I still have the problem on OSX using the standalone adapter. I think I've heard that Apple knows about this bug as well.)
I probably could have repaired the filesystem under Linux with fsck if I'd used the standalone adapter. I didn't test that -- since I was able to fix the fs under WinXP, I decided to quit while I was ahead. I may do some more tests later so I can provide some bug info to Apple and iRex.
As a side note, a common symptom of this kind of filesystem correuption, in my experience, is that shell access stops working. I'm not sure exactly why that should be, but when the filesystem gets corrupted, the application folders stop acting like applications and just open as folders.
Just thought I'd share....