Missing directories on external disk after re-imaging system


I've been using dd to image /dev/mmcblk0 to /dev/sdd and the process is working as far as that disk goes i.e. the router boots, everything works fine, except...

If I also have directories on /dev/sdb, after I create the imaging those directories are present, but if I copy the image to anther disk and then use that disk to boot from, the directories on that external disk disappear. This happens each time.

Is it a permissions issue?