For any root-related or Cyanogenmod-related questions, you might have better luck on the XDA-Developer forum.
My NC is not rooted anymore, so i don't know if this will help. My books are under:
If I remember correctly, this was also true when I dual-booted. I did occasionally get confused as to which directory I was on, but you seem to know what you are looking at.
Thanks, but "no prize"!
This is becoming a real mystery as finding th 1.4.2 titles on the sdcard is a "piece of cake".
I am starting to wonder that, when splitting the eMMc into two sections for my current setup, the "files" section isn't showing.
I do have this question up on "XDA" also.
I have placed my kindle compatible books in the \kindle folder on the uSD card and the Kindle app finds them there.
Is this what you are looking for?