It's been a while since I used a Whisperlite - in fact, I stopped using it when I got a .9L MSR Titan Kettle. As I recall, one reason was because it wasnt' broad enough to fit on all three supports: to be solidly on two, it didn't quite reach the third, which meant it was lopsided and one side rested on the burner instead of the supports.

Like I said, it's been a while since I tried it, so I may be remembering wrong. But the point is, be sure to make sure the pot is broad enough to sit firmly on the supports.