Alright, I deleted the native vlan statements from both ports on the Juniper6 side. They now both look like this:
mtu 9216; unit 0 { family ethernet-switching { port-mode trunk; vlan { members VLAN100; } } }
This hasn't made any difference.
I had thought to restart the switch at some point, I'm going to do that now. I doubt it will make any difference.