For electrical engineers : Noise problem?

What was the the shielding connected to ? If there is no common reference point, you cannot shield against noise, as it would effectively act as an aerial and induce high speed transients into the cables. By connecting them to a potential, you have a signal return path and have eleiminated the noise. If the signals are not referenced to ground in any way, shielding it to this point is ineffective, as you have found.