Presumably from go over (“to be received”), used as if literally (“to travel above”): a lead balloon would not travel well through the air.
"go-over-like-a-lead-balloon." YourDictionary, n.d. Web. 17 August 2018. <http://www.yourdictionary.com/go-over-like-a-lead-balloon>.
go-over-like-a-lead-balloon. (n.d.). Retrieved August 17th, 2018, from http://www.yourdictionary.com/go-over-like-a-lead-balloon