They don't. It only looks that way from your end. My roommate also plays D2, and when I use BO (or any casting skill for that matter), it looks normal on my comp, but on his comp, it looks as if I'm casting BO twice at the same time.
Although FCR would make your spell casting faster, and thus you'll see more of the projectile, seeing two of any skill shoot that quickly is just an image/graphics desynching issue. It's a lot more noticable when you're slightly laggy on a Sorceress using Frozen Orb. If you just hold down right-click (to cast), sometimes you can shoot what looks like two orbs out, but clearly the 1 second casting delay would never let you do that. Your mana also will not go down by twice the mana (for casting two orbs) nor deal double damage to whatever is in the orb's path.