Maybe it's not the type of stretches you're doing, but the intensity and amount of time you are holding the stretch. I think a lot of people tend to overstretch, either by holding the stretch at a position that is past the optimal point, or by holding the stretch too long. Also, I've noticed many people bounce into the stretch. This is a definite no-no.
What is optimal? I'm not sure. This is an on-going debate. However, make sure you are not stretching to the point of pain. This is not a 'no pain, no gain' thing. You need to get to a point where you can feel a comfortable stretch and hold it for no more than 30 seconds. Then stretch the opposing muscle group. So I would do the calves/hams for 30 seconds, then move to the quads for 30 seconds, then back to the cavles/hams. Don't expect to be more flexible overnight. Through a consistent stretching program you will become more flexible over time.
I'd also add a piriformis stretch. Doing dead lifts and running can tighten the buttocks area. This will losen things up around there. Here's a good description:
http://www.rice.edu/~jenky/sports/piri.2.html
Phil M.