The first thing I'd look for is an issue in the tracks where the channels powered by the Z4000 handles are either connected together somewhere or the loops themselves are connected to the TIU channels in such a way that they are out of phase with respect to each other.
Disconnect one handle of the Z4000 from its TIU channel input and connect the other handle to both of the channel inputs. If the problem goes away then the loops are possibly connected somewhere. If the problem persists, I'd look for the loops being out of phase with respect to each other.
