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Wait is your big one set up as a 2.4 or a Trident? Eventually I am looking to build a 2.4 version with a 600mm cubed
work envelope (or bigger). Just not this round. LOL

Well, I had a good look and compared it to NoJo's config but I'm afraid I can't wrap my head around the problem.
If i understand spindle synchronized motion correctly then it really only depends on the encoder signals connected to the 'spindle.0.' pins.
I think the most likely way figure this out is to diagnose things with hal scope on the machine and find out what is happening to the index-enable signal and z-axis motion.
I'd love to help more but I have no hardware to test any of this.