Okay then - so far, I've done the following non-destructive things
-Check to make sure your metadata writer plugins are enabled
-Reboot your computer.
-Shutdown your PRS-600 via menu then turn it back on.
-Try using a different SD card.
-Try just using internal memory for a while with the SD card removed.
All good, but transferring things back onto my SD card, still means no collections carry across
Internal memory, it still comes up with some of the weird naming things.
Tried two SD cards, and the problems the same. I do note that sometimes Calibre takes a long time to do things - I wonder if something in the reader 'times out' after a while, and loses the collection info?
I'm going to factory reset the reader, and also do the following:
Format your 1 gig SD card. ###This will wipe everything off of your SD card.
Format internal memory via menu. ###This will wipe out all books on your device.