Tiger used his Scotty for many years after switching over to Nike. I would also guess that his switch to the method could be attributed to his sponsor flee fest, after his escapades came to light, and Nike essentially "forced" him to put that Method putter in his bag. Rory's putter and the Nike Method have a completely different feel and could possibly roll quite differently of the face.
Once a player of that caliber gets used to a putter and has some success with it, it can be very hard to change. Plus when things are not going very well sometimes players will look for a spark or something that feels a little more comfortable, maybe why the Scotty went back in to the starting line up for Rd.2.
I don't know what his contract details are but I am sure he will play whatever it is that he feels will give him the best chance to win, and is most likely outlined in his deal. I chalk this less than Rory-like performance up to a little rust and the first tourny with some new sticks. Give it some time. If in 4-6 months time from now if has not done anything we might be able to start looking to the gear as a problem.