sorry sometimes it thinks your posts are spam (if you have more than 10 posts) and they go into a waiting list until i approve them.
usually free probe is very small and runs to the bottom even on high percentage gels. How big is your probe in kb or bases?
Non-specific competitor is good to add. However how much protein are you adding from your nuclear extract?
After centrifuging you should re-suspend in suitable buffer for EMSA similar to your binding conditions. Have you optimized the binding conditions for your specific protein? What pH does it bind the most? What [salt]? What buffer did you use Hepes?
Sorry for the many questions however EMSA is quite specific to the protein and probe!