No luck still John?
I only get the disconnect sound if I use the windows eject device option - no sound for calibre, not sure about the desktop as I haven't used it for a while.
But as yet I haven't experienced the errors you have been getting from incomplete ejects using calibre. I have logged a couple of calls on other things to do with calibre on the KT (fixed margins and not transferring to device cleanly). I have not had a positive response from Kovid - he has said that the KT is "buggy" and that they won't be actioning the requests. Perhaps this is one of those bugs he means.
Hope you can get it sorted