My guess is that you are running into the problem described in this FAQ:
[Android] I have added a lot of books and now adding books takes forever. What do I do?. My thought is that you have reached a point where it is so slow that the network connection is timing out, but as you didn't say how many books you have already transferred I am just guessing.
If you send me the CC and calibre debug logs (
how to do this is explained in this FAQ) I will see if there is more detail available.