I think people in this thread are underestimating the degree to which Senate races are independent of Presidential ones. They're correlated, sure, but not excessively. Remember the coattails in 1972 and 1984? Thought not.
Speaking of whether this has ever happened before, have either chamber of congress and/or the Presidency flipped in opposite directions? The closest is in 2000, where the Democrats gained the Senate for the lame-duck period only (and then when Jeffords defected, but that doesn't really count).
In 1916, The Republicans won the most seats in the House, but the Democrats held control thanks to a few minor-party candidates. Aside from that, it appears not to have happened since the beginning of the 20th century.
