It isn't clear to me what is failing, when.
First, upgrade CC to V3.2.5. V3.2.4 has a problem where sometimes wireless device connections fail.
So, back to your problem. If I understand correctly, there is a computer somewhere on your LAN running calibre. Your library is not on that computer, but is instead on a NAS on your LAN, connected by cable to the computer running calibre. Your Transformer is connected via wifi to an access point that is connected via cable to the computer running calibre.
If this is correct, then the first problem is that calibre specifically does not support putting the library on a NAS. See
I am getting errors with my calibre library on a networked drive/NAS? in calibre's FAQ. All sorts of strange things can happen, and what you are seeing might be one of them. Put the library on a hard drive directly connected to the computer running calibre and see if the problem goes away.
If the problem does not go away, then ...
It seems that you are saying that the entire computer running calibre is hanging ("No other PC programs or PC desktop shortcuts respond"). This indicates that the problem is somewhere deep in the OS, because there is (in theory) nothing a user-space program can do to stop the OS. I have no idea what the problem might be.
Some diagnostics:
1) Does the same thing happen when you connect to that content server from a browser on a different computer? From a browser on the same computer?
2) Are there any errors in the content server logs? (use Preferences -> Sharing over the net to see the logs).
3) Does everything appear to work until you disconnect?
4) If you wait for at least 2 minutes, does the computer come back? This is checking to see if the problem is related to system-level TCP network connection closing, which has some timeouts in it of slightly in excess of one minute.