Are you using PHP within a web server, or running PHP code on the command line?
If within a web server, the problem is that the PHP code runs under the user of the web server (e.g. apache or httpd) and this is not the same user that you have used to create the blockchain. So the ~/.multichain/ directory points to a completely different place for that user.
You should not have a problem if you're running PHP on the command line, but please let me know if I'm wrong.
And if you want to run it from the web server, make sure the blockchain directory and multichain.conf file are readable for the user which the web server is running under, then use the -datadir option with multichain-cli to choose the appropriate directory for the chain you want to use.