Which storage provider are you using? Also, could you please provide more details on "After performing a restore and doing a diff on the original files and restore, all the empty directories were missing." situation?

I'm using local filesystem as the storage provider. As far a more details, I backup directory tree that has about 17K files, including directories that are empty. As a test, I did a restore to /tmp of this directory, and my expectation was that the restore would be identical to the source. This is not the case as doing a recursive diff on the two directories shows differences. The differences all being that any directory that was empty, was not restored.