You probably put in the longer screw with enough force to strip it in the center threads so the threads below the part it is screwed into is is probably keeping it there. Two thoughts:
1) If top access is good - take a heavy pair of wire cutters and get it's jaws under the head of the screw between the track and the screw head,and squeeze the handles fairly tight. The V shape of the jaws should act as a spreading device between the track and the screw. Don't squeeze so hard as to cut the top off the screw. Once the pliers are under the head of the screw and you are sqeezing the handles to put upward force on the screw - try to unscrew it using the cutters for upward assistance. Be careful as you turn the screw it might tend to slide the cutters out - scraped knuckle time! It has worked for me.
2) if you can get under the track and see the bottom of the screw as it turns - use a dremel tool to cut the bottom off the screw and remove from the top.
PS if#1 works - it is quick and you won't swear much!