I'm glad it all worked out.

About your question...
Do you mean that the Flash video is showing above the the lightbox when it pops up? I'm not 100% sure about this, but I think this is a configurable option with Lightbox. By default, I believe lightbox removes all Flash objects from the page and then displays lightbox.

So, if that's not working, maybe consult the Lightbox documentation for how to configure this.