perhaps your image projection input or output parameters are incorrect, should be something like fisheye to equirectangular, but i am not even sure if skybox supports re-projecting arbitrary fisheye lenses so you may need to use an app like kolor auto pano video or video stitch etc
also see re:lens plugin for premire + AE
http://revisionfx.com/products/relens/
and dome to rect tool and plugins
http://www.andrewhazelden.com/blog/2013/08/dome2rect/
http://www.andrewhazelden.com/blog/2012/11/domemaster-photoshop-actions-pack/
sam