When I Sit At My Desk For More Than A

when I sit at my desk for more than a few minutes with my legs crossed, I've started to have pain once I get up and start walking. the pain comes from the inner left side of my right knee. its a matter of how I position my knee that makes it hurt or not. I'm a regular at the gym and just two days ago I did my lef workout with no problem. so, going up and down is no problem, its the sideway motion that causes pain. What should I do?