Update:
we tried on multiple Fedora 19 and Ubuntu 13.10 machines and we reproduced the problem on one of them. The description you gave matches 100%. The source of the problem is in the USB kernel module. Unloading it fixes the CPU problem.
Edit /usr/NX/etc/node.cfg and set EnableUSBSharing key to “none”. Restart the server with /usr/NX/bin/nxserver –restart. Please confirm that the workaround works.