I've watched him pitch and I've looked at the numbers and I've listened to him talk and I cannot find an obvious sign that Cole Hamels is anything other than a pitcher who is slightly out of rhythm. I mentioned this on Twitter and I will reiterate it here: the guy we've seen through the first nine starts of the season looks a lot like the guy who was on the mound for the first third of the 2010 season. When he misses just off the plate, he does not get the call, and when he misses on the plate, he gets clobbered. He has gone most of the season without pitching with a lead, which I am guessing does not help matters. But his velocity has not changed, nor has any other telling rate stats: swing-and-miss, ground ball, etc.
Check out the following two sets:
Hamels through nine starts in 2010: 57.1 IP, 60 SO, 20 BB, 10 HR, 25 ER, .95 GB/FB, 12 % swing/miss, 19 % called strike
Hamels through nine starts in 2013: 56.2 IP, 47 SO, 24 BB, 9 HR, .96 GB/FB, 12 % swing/miss, 15 % called strike
The most significant difference is the strikeouts, but that does not appear to be "stuff" related. Rather, it is because he is getting fewer called strikes, and thus has found himself in fewer strikeout counts and better hitters counts.