Which confirms it is not a Calibre issue. Although fsck.vfat does not seem to report errors, it is still possible that formatting would help. However, first I would try other possibilities - it may be your automounter (HAL or whatever is in your version of Ubuntu) causing the problem.
You seem to be at least a bit familiar with command line, so you could try mounting manually in rw mode:
Code:
sudo mkdir /media/sony
sudo mount -t vfat -o rw,remount /dev/sdd /media/sony
sudo mount
The first command creates a manual mount point, the second command mounts the drive in rw mode to the created mount point and the third command just tells you whether it is really mounted in rw mode - it would contain 'rw' in the line with /media/sony mountpoint. You can try and see.