When you just flop the bypass over you shouldn't hear a metal sound, more of a thump, but when you push the bypass handle all the way past the cam over point and it locks in place you can sometimes hear a more metallic sound. Like a click. Don't worry about the sound. Worry more about the quality of the seal.
I gave that one some thought and maybe the sound they were hearing was the rod "catching" the plate and the vibrating sound that it would make while the rod cammed over a bypass plate that was not pressed firmly against a gasket.
I realize my description is probably clear as mud but I suppose if it was as out of adjustment as the op described it would sound very different from what we are familiar with.