On line 411 in Intersection.cs when c is calculated, I believe it should say:
float c = kee * (kgg - radiusSq) - keg * keg;
float c = kee * (kgg - radius) - keg * keg;
The difference being radiusSq instead of just radius. I noticed this first when I was having troubles with intersecting segments with capsules. I would post a screen shot of the problem but it's getting late and I don't feel like it:) So hope that helps!