I know it boosts Aura and Pulse moves but I have seen Water Pulse confuse the opponent almost every time it was used from either Mega-Blastoise or Clawitzer.
Nope. It's just luck you have. Mega Launcher boosts these moves by 50%: Dark Pulse, Dragon Pulse, Water Pulse, Aura Sphere, and Heal Pulse. For Heal Pulse, instead of healing 50% Hp of your ally, it restores 75% instead. Hope I helped!
The confusion is just luck, and mega launcher doesn't effect the confusion chance.
Hope I helped