I have no explanations (I want to know why I'm less flexible after having kids!) but something that might interest you is reading the R/N post below about Fearing the Squat no more. I do know that doing the squat does build up some flexibility, to how much over time I am not sure. Yoga and Pilates do wonders too if you like those! I do myself, but have not been doing either of them regularly. Also, amazingly jumping on a rebounder increases flexibility as well.
MSM might be of help too, I've taken it after exercising and lifting heavily and never got sore because it was building and rebuilding the muscles so quickly. I was taking a few teaspoons a day by that time. Hope this helps :) Caitlin Lorraine