Accessing windows server deduplicated files from other operating systems

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)

The System Volume Information directory should be excluded using the /XD switch. Probably a good idea to exclude other hidden/system directories such as $RECYCLE.BIN.