No idea whether this will work, but I figure it can't hurt:
Try going into the android settings (not the Sony ones, the android ones showing on page 3 of the homescreen) and see if switching 'USB Debugging' on or off helps any.
Haven't had this issue on my reader, so can't comment on the specific case, but had much the same happen on my Android phone and switching USB Debugging a couple of time seemed to fix it there (still not sure why, but it seemed to do the trick...)
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