Ahh – Thanks @anton and @minghangli the instructions actually point to the dev-1deg_jra55do_iaf branch (to reduce the number of branches that need updating) - so this may be the issue!
@Paul.Gregory – when you rerun, can you please try switching which branch you download
Under the heading
“Download your other configuration files from an ACCESS_OM3 run”
Can you swap
mkdir -p ~/access-om3
cd ~/access-om3
module use /g/data/vk83/modules
module load payu/1.1.5
payu clone -b expt -B dev-1deg_jra55do_iaf https://github.com/ACCESS-NRI/access-om3-configs/ access-rom3
cd access-rom3
To
mkdir -p ~/access-om3
cd ~/access-om3
module use /g/data/vk83/modules
module load payu/1.1.5
payu clone -b expt -B dev-regional_jra55do_iaf https://github.com/ACCESS-NRI/access-om3-configs/ access-rom3
cd access-rom3
The remainder of the instructions may be a little different as the original text that you are changing will be different (and some of the changes may now not be necessary).