It's me who should be apologising as I should have posted the solution that I found!
Seems Microsoft made a change to the Teams app which runs on these phones and now the layout is controlled by the type of licence assigned to the user.
We used to assign Teams Room Standard, but after adding some "Microsoft Teams Phone Resource Account" licences to our tenant and changing the user assignment, the phone layout changed back to the one we were used to. Note that you must also sign out and back into the phone using the resource account to action this change.
I think you can add 20 licences to your tenant on a 90 day trial basis if you'd like to test, but I can confirm this has fixed the problem on 23 of our phones now.