Well, having power (voltage) is not the same thing as having a good DCS signal and I'm still not certain from your answer if the upper and lower loops are electrically separated or not - should be just a yes or no answer. You say the upper is fed by a ZW and the lower by a Z4K - if the loops are electrically connected are the transformers in phase ?
You could try Joe and RTR12's suggestion to cut the lower loop tracks into blocks and see if that helps, but I think you first need to determine if the lower loops are getting a good DCS signal. I would also find unusual that one set of tracks fed from the same TIU would not need blocks and work fine, but the other would. If that's the case then there might be something interfering with the DCS signal on the lower loops.
