The reason I asked if you have any other problems is because a lot of DUP ACK's could be caused by a bad (physical) link somewhere in the chain. A bad wire, or a cable that's too long, crosstalk, ... But then I would expect you to see other problems on the site too, not just the site-to-site VPN. I'd try to test another protocol just to see if it's SMB specific. Also, what bandwidth are the WAN links on both ends?
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