Machine is trying to move to new position just after lcnc startup

Apologies in advance, I'll probably describe this wrong but hopefully the video makes it clear. 
I'm in the early phase of a Weeke router retrofit. I've got my Delta Ethercat drives up and running with LCNC thanks to a lot of help over in the Ethercat section of the forum.
I've got an issue at the moment that I think is probably just basic Lcnc behavior stuff. After I launch Lcnc and Axis loads the axis positions are updating and the machine is trying to move to that new position (if it's enabled at the time). It seems to happen just as the "axis" dialog box in the bottom right corner disappears If it's not enabled then the position for the axis update and everything is good from then on. It looks like Axis is importing the stored values from linuxcnc.var about 5 seconds after startup, the g54 values I think.
If the machine is enabled at the time when the update happens the drives are seeing this position update and trying to teleport to the new position at what seems to be max speed and acceleration making for some very noisy and unpleasant sounds. 
What do I need to do to get rid of this behavior?

Video shows it all pretty clearly. Even though you'll hear me saying that it doesn't do it the first time it clearly does. You can see the Z axis (I think) move about 50mm right at the start of the video.

While it's certainly possible that it's related to EtherCat, I don't think so. The machine movement is absolutely rock solid and silent and so long as I don't enable the machine until Lcnc has updated the position values.
Lcnc is changing the machine start possition after it loads and it looks to me like it's loading the g54 values from the linuxcnc.var file about 5 seconds after it loads. It seems to correspond with the axis toolchanger message in the bottom right disappearing but that could be purely coincidence.
The 'jump' occurs every time I restart Lcnc but I'm not powering off the drives. If I set the drives to display encoder count the value doesn't change when I close lcnc so if it were an encoder feedback issue I'd expect to see changing values on the drive its self.
It seems more like an issue of incorrectly saving machine coordinates on close or load.

I've found the EtherCat experience to be absolutely positive so far. I had this retrofit up and running (with a lot of help from the forum) in a day or so compared to about a month on the previous machine.