A little more info… when you press ‘define zero’ on the z-axis page, it sends a command (G10 Z0) to tell the controller the z-axis is at 0. Then it sends a G00 Z.25, if in imperial units, or G00 Z5, if in metric. I haven’t seen an error cause by the z-axis not keeping up before and not sure it’s monitored. So, I suspect it’s a sled issue and even though the sled isn’t moving, the check is probably still happening. I think the problem might occur when you ran the test motors/encoders. I suggest resetting the chain lengths and trying again.
Did you mark your chains when you fed them out initially?