Well I do have a Linux AD server. I also have a WinServer2008R2 for 6 months, 
but it's having issues connecting into the domain for whatever reason. I was 
referring to the SSH encryption. I don't recall Samba using encryption for file 
transfers, just for user/pass, maybe even just pass.

Are you using the stock DeltaCopy files? Those are really aged. Here, I 
uploaded you some newer files. Stop the DeltaCopy service first and put these 
in. Feel free to make a copy of the old files. Tell me if these are any faster. 
They should be. 22-23 hours to backup a server? That's a LONG time. The longest 
I've gone was 21 hours and that was just recently during an incremental bc 
BackupPC was suddenly being stupid about backing up my Windows machines because 
it felt like it.

Here are newer files: http://badmarkup.com/deltacopy/

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