I have only just received my Touch. I spent the 2 plus weeks waiting for it to arrive obsessively reading MR to learn other's experiences. After reading the posts about issues with Calibre I was very careful when I loaded my books. I started one at a time and progressed up to 5 and then (feeling reckless!) 10 ebooks per transfer.
I allowed plenty of time for them to transfer waiting 20 to 30 seconds after the "job" was supposedly complete before disconnecting my Touch. I used the Calibre disconnect waited 20 to 30 seconds and then checked with Windows before actually removing the USB. Only once was I still connected when I checked with Window and that was when I didn't wait before checking.
Loading 250 books this way took quite a while but it made me be ruthless with most of the 150 freebies I have collected over the past year. They are still in my Calibre library but haven't made it onto my Touch.
Most but not all of my covers made it across - probably 10 or so from the 250 books. However most of those covers were missing on my original Kobo as well. I have never understood why this happens as I have attempted to redo the covers several times. Sometimes it works - sometimes it doesn't.