I believe the problem is the track output of the Z-brick barrel jack is opposite - the center pin is common and the outside of the barrel is hot.
The 14 volt accessory output is clearly marked.
The track power gets correctly phased with accessory output when using a Z-controller or the MTH adapter cable to supply the input of the TIU.
When a Z-brick is plugged into a TIU as accessory power for the TIU, it is phased internally.
JOHNGALTLINE addressed this already.
How have you connected the Z-brick to track power?
Phase the output wires of the brick to the accessory posts of the same brick. Then, phase any other AC transformers.
All scenarios should work well after that.
here's the phasing process from the 1954 Lionel Operators Manual