As I've said, there are multiple reasons. I listed one of them. I find that the most frustrating, because the surface is painfully slow (to me, just in case you ask me to prove it), and that's perhaps why that was the first and only reason I pointed out. But now that you're asking nicely instead of laughing at my answer as if it were stupid, I'll answer just as nicely:
There are multiple reasons why he has been less successful there. Some of them, in my opinion, are:
1. In his prime, he didn't care very much for it, because he was more concerned with Basel and WTF, which led to him skipping it in his best years (2004, 2005, 2006)
2. Back in the mid-2000s, the Masters weren't seen as important as they are today (this factors into 1)
3. Once he started caring for Masters seriously (which was around the point he stopped winning Slams), the surface became very slow, which isn't conducive to his game