Super Tight Knees - No Running for Me

Went to the gym tonight and favored my knees.  They are so tight.  I walked the warmup and cool down laps.  I can't straighten my leg or pull my toes up.  Tried to not put my full weight on the right one.  It seems to be the one bothering me the most.  Luckily, the workout was mostly upper body.  I did some of the squats hoping it would stretch the area that was tight.  Sure hope I'm not doing a bad thing by going on with my activity.  Saw something online about Baker's Cysts.  Uggh.