Same synced drives, different remaining space - aaarrggghh!

This may not pertain to Mountain Lion exclusively, in fact i know it doesn't, but nobody (not even the manufaturer can explain this:
I have two 2TB Western Digital Caviar Green drives both formatted on my mac pro.
I typically use Decimus Synk to sync the drives.
One drive reports 1.16 GB available
The other drive reports 53 MB available
Each of the 46 folders on the drive report being the same size in Get Info.
I've backed up, reformatted and copied back the contents of one drive using simple Finder copy (drag and drop) and still have this issue.
Any ideas?  This has happened with other drives too.

OmniDisksweeper may help you find out what's going on.

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