Could my inflexability be caused by a medical problem?

For my whole life I have never been the most flexible person ever, however it seems that lately i am even less flexible than before. When i bend down i can barely reach my knees among other very pathetic things that i cannot do with my body like sit with my legs straight out in front of me. Whenever i try, there is immediate extreme pain that shoots throughout whatever i'm trying to stretch (mostly my calves and upper legs). I am a very athletic person and underweight but i still am not flexible at all! I do yoga twice a week and even the guys with the beer bellies that take the cl can bend further than i can. i am worried that there is something wrong with my muscles or joints that is causing this problem. (i can pop my joints very easily and it seems like something is always cracking when i move) Also, sometimes my muscles (in my arms mostly) will be very slow to expand when i extend my arm and it feels like my veins are tearing. I am fairly short, if that has anything to do with it... and have a degenerative bone problem in my jaw so i'm worried that my other bones could be doing the same? i just have no idea and am sick of being this way, any help would be greatly appreciated!