Windows Server Backup (2012) to Both Local Volume and Remote Folder

You are right in your assumption that WSB has created shadow copies. It uses these copies to maintain a backup history.

If you still have backup versions (and thus shadow copies) of points in time before your dedup optimization job has run, you would not see any savings at all since the deduplicated blocks have not been freed - they are needed for an older, non-deduped version of the data which is still referenced by one of the shadow copies.

So the bottom line is that if you need deduplication savings to show, you need to remove all older shadow copies.

The increase you are seeing is probably not due to deduplication activity but simply due to the fact that additional backup jobs were run in the meantime and older shadow copies are not deleted unless necessary (i.e. the volume would not have enough space for the new backup otherwise)

That article you link is wrong. There is no way to specify the retention policy in Windows Server 2012 when backing up to external disks. I don't know why they lie like that... The configurable retention policy feature DOES, exist for the Windows Online Backup feature that you can use in Server 2012. Possibly this is where the confusion arises.

AFAIK backup disk space usage is the same in 2012 as in 2008 R2, which was also supposed to handle retention automatically, but didn't always work. When this occurred in 2008 R2 we would use the Diskshadow utility to manually trim VSS versions from the backup disk, which is what I'd advise you do here.

Use diskshadow to delete oldest VSS copy from Windows Server backup disk: http://www.bluecompute.co.uk/blogposts/windows-server-backup-manually-delete-snapshots/

EDIT: As Twisty points out, Diskshadow is not needed for this any more, you can use the new WBADMIN DELETE BACKUPS command