Ok got it, i wasn't expecting such an elaborate filesystem caching on a device with 500MB Ram.
I did some testing that supports that hypothesis.
When I copy a 50MB pdf onto the device i can open it and its still intact when I connect the kindle to my computer and open it there. However when I copy the same pdf 11 times (to make sure I max out the ram) all of the files are toast.
So i guess its time for a new ebook reader
