Well yeah, in a handful of games or so they look awful defensively. But that will happen. When you compare them to the past 3 years, their defense has been pretty bad. Game by game basis AND stats wise. Just trying to give some perspective. The stats show they are much worse than in the past, which your observations agree with.
But if your going to use FG% with the rest of the NBA, you might as well use Points Per Possesion. I know its tough to decipher in the game, but the human eye can only see so much. From watching every single game and looking at the stats, the Spurs are clearly worse on defense than past seasons, by a wide margin. But when comparing to the rest of the NBA they are still elite.