I had the same thing happen once. I believe they use different file systems but I'm not sure. Anyway, I could see that the memory was accounted for but the pics wouldn't come up after I used the card in my pda.
Did you try scandisk on the CF? I had my CF corrupted when I had an error in the middle of movieplayer and after I ran scandisk to fix the errors, all my data was restored. (Of course I copied the files to my desktop, reformatted the card and put everything back on it for safe measure though).