It's likely a culmination of a few different factors. It seems like with softer shoes , you hit the ground harder. A bunch of studies have shown that same effect. One group even did it with load cells implanted directly in people's knees and showed that the knee force is higher. Depending the shoe, some are even designed the change your running form, and that could increase your knee loads, too. Lots of shoes out there these days that make it feel like you're wearing sketchers shape-ups.