Leg pain after switching to shorter cranks

[choochoo]

I recently switched from 172.5mm cranks to 165mm.
I've done a couple of 30 miles rides since the switch and i've been experiencing some knee soreness at about the 20 mile mark. Yesterday, I was on the trainer for 30 minutes and I was getting some knee soreness and also some pain in a muscle above my quads. I wonder if my knees are coming up that 7.5mm higher is causing this.
I'm generally not that flexible of a person. I should be stretching more. I should go for a bike fit too since my bike is fairly new to me. But has anyone ever experienced this with going to shorter cranks? I haven't changed any other positions. I might raise my seat a little to see if that helps.