They definitely do with the under-surface being frozen. But if it would make an impact on a runner, I am not sure. Is it perhaps your body's lower temperature may have something to do with achy knees?
PS I admire your early rising training discipline. I should get into it.
I was being facetious.. I'm quite sure it was probably the cold, felt fine an hour later..
Gravity is stronger, because the cold makes the earth shrink, and you're therefore closer to the center. So you're effectively heavier.