I did find a way to get rid of those extra copies the sync function put on...use Calibre!
Sony had a good go a redoing up to 4 copies of the same book next time I attached it, so I will be turning off the autosync function as described above.
One thing I have struggled with is getting purchased ebooks straight onto Calibre without using the Reader Library software as an intermediate step. Here in Australia we don't have the Sony bookstore but buy things from Borders or others. The files mostly seem to come as a URLLink-somenumber.acsm which I then have to locate in the reader library and transfer to Calibre. Does anyone know any faster ways?
Or any way to stop the Reader library automatically openning when you attach the device on a mac?
Cheers