Well, initially, it was the failure of Rodriguez and his team-mates to respond to Contador's move that allowed him to get away and open the gap. That was just a lack of tactical nous on Katusha's part.
Then Contador got help from others in the breakaway group - not only team-mates but the likes of Tiralongo too - while Rodriguez got absolutely no help at all, especially not from Valverde.
This also explains why Valverde was able to ride away from Rodriguez and chase down Contador towards the end. Plus Valverde had team-mates to assist him in the chase, while Rodriguez was left with two Saxo riders just sitting on his wheel, sapping his morale for mile after mile.
When you look at it that way, it's not only plausible that Rodriguez lost so much time, but to his credit that he managed to limit the losses to two minutes - he did seem to be rallying a bit towards the end and as Contador visibly tired, at least Rodriguez managed to stop the gap getting any bigger.
So, all very believable and not necessarily indicative of Team Saxo having enjoyed a nice barbecue on the rest day.
But not proof that they're riding clean either.
That's my take on it, anyway.
d.