On inspecting the logs I found that after the controller had come up it had "upgraded" to the officially released 2.0-beta12 from the devel PPA. This is very surprising and is almost certainly a bug. When --upload-tools is used it's those tools that should be used.
When testing a customised version of Juju 2.0-beta12 and I bootstrapped like this:
juju bootstrap foo lxd --upload-tools --auto-upgrade false
On inspecting the logs I found that after the controller had come up it had "upgraded" to the officially released 2.0-beta12 from the devel PPA. This is very surprising and is almost certainly a bug. When --upload-tools is used it's those tools that should be used.