Your problems are very strange; certainly with 1.03 I've done large (ie, 20GB+) syncs in one go with no problems, over both USB and Ethernet.

The sync protocol is not really designed for ethernet though; there is an extension which uses a separate socket connection to send the file data (much like FTP) but there is still plenty of unnecessary work going on - the sync protocol itself deals with a lossy, error-prone link (eg, USB with flaky usb slave controllers like...errr... most of them).

Hugo