I have no idea if my issue is the same as your, i will copy my post. For whatever reason my new E9 AA will not run well on my ZWL. Runs great on my Z4000 and PW ZW.
I had the same issues sometimes I would hit the horn for the AA and one would stop but not the other. No idea if you have another transformer, but worth a try. Worked for me, no problems now, just can’t run it on two of my tracks.