Examine your ruler carefully. That's how I figured out I was shaving the ruler when I cut. I *thought* there was a curve in the ruler and proved it by butting it up against another ruler I hadn't yet used for rotary cutting.
Edit: Oh, and with flannel, I prefer to *heavily* starch flannel before cutting; otherwise it moves around on me. I use a 1:1 solution of Sta-Flo liquid laundry starch and water.