I've definitely had this bug for a while too, (since 1.1, I think) and also recently had a bug where mod command pods would shake on launch, but remain fixed above the launchpad, with the rest of the craft flying through them on stage to launch. Upon going through all my mods to eliminate the problem, it seems this one is the culprit. Staging works fine now, and the lighting effect is gone. Has anyone else had the weird launchpad bug? I'd love a fix if there's one to be had!