Hello!
I must admit that I still have a problem with CF card reader.
Could you write me exactly what model you use?
I use 
http://programatory.com.pl/sklep/index.php?p40, adapter-cf-ide-v-1 and is very unreliable.
Reads only one SanDisk 1GB. Does not read any other card (4GB etc).
It is very uncertain, and to read only certain files.
Maybe the size of the cards is the problem? May be less than 1GB?
Please write that you are using an IDE -> CF Reader.