Tried applying them from the command line but of course package manager then doesn't know that they have been applied.
So I tried the package manager installer again and now I see the problem. The installer only offers me the 4.6.1 to 4.6.2 and the 4.6.2 to 4.6.3 upgrade files.
So to fix this I need to get the package manager to offer me the 4.6 to 4.6.1 upgrade.
You can run everything from the command line, and then run the old installer page (/acs-admin/apm/packages-install) to install the package but uncheck the sql scripts. This will get the master number back in sync so that things will be normal going forward.