The issue with DVOA (and really, any rate stat) when it comes to the Patriots running game is that they are a gameplan team that runs a lot in advantageous matchups and does not run in disadvantageous matchups. So when they play the Ravens, they might run the ball 10 times and throw it 50; against the Colts, they run the ball 40 times and throw 20. It looks like they're awesome running the ball because the overall efficiency is very good, but the numbers are skewed because they don't run against teams when they can't.
There is something of that effect going on this year - they ran for 190+ yards in both meetings with the Bills, who were 31st in rushing defense DVOA, but I think you're right and they've shown more ability to run against top Ds. They went 29 for 99 against Denver (#2 rush D DVOA), 19 for 80 against Carolina (#6), 25 for 118 and 38 for 147 in two meetings with the Jets (#11), and most recently, 27 for 102 vs the Titans (#7). So they've run the ball fairly often and with reasonable effectiveness against just about anybody.