I looked at your loft, and I think I see the issue. If you look at the wireframe, it's trying to map the inner part of one circle to the outer part of the other:
If you go to your sketches, you'll see that when you created your circles, it numbers the circles edge1 for the first outer circle, then edge2 for the second inner circle in the order they were created. But when you created the second pair of circles, you reversed the order in which you created the circles so the outer is 2 and the inner is 1. I believe when you loft, it tries to match the edges in order. You'll be able to see this in your loft when you mouse over the sections, it's kind of split into two. Not sure if this is considered an "invalid" loft, but it did let you make it.
To fix this, you'll have to go into one of the sketches and delete one of the circles, and make sure the order matches. Then you'll be able to pad either side properly.
So the larger circles at the bottom have their wall reversed, and when you try to pad that, it gets confused.