So I wanted to see if the z stage had finished moving up before starting to move to open. So I got the camera out to take continuous mode pictures about 0.1 seconds apart.
The first set here is the default mode as the above parts were printed:
The second set is using the command line command "d300" to "Breathe Delay set to 300":
The third set I reset the machine to default and rechecked it was back at default, then I used the command line "j500" to "Reposition gap set to: 500":
The first set does show it does start to move the slide before it has finished moving the z stage. The evidence doesn't really show it being a definitive problem though as the VAT wouldn't really start to move much until it is almost done moving up in Z.
So I do have a fix for it though if that is the problem. I'll need to try another print after looking at something else first though.