At the bottom, MikePerry says " ... you need to either edit the Torbutton about:config prefs 'extensions.torbutton.socks_host' and 'extensions.torbutton.socks_port', or set the environment variables TOR_SOCKS_HOST and TOR_SOCKS_PORT before starting TBB."
I tried doing that and it also did not work. I may have missed something very obvious though.
I downloaded an older version of Tor to see what the TorButton custom proxy settings changed. I've been able to replicate that now using the latest version of TorBrowser. I've modified TorUser's answer (which was inspired by mimir's answer).
Here's how to run multiple instances of Tor Browser on Windows since the 4.5 update:
Optional: Download, verify, and install Tor Browser.
Make copies of the Tor Browser folder with different names (eg. Number them)
Launch Tor Browser
Modify extensions.torlauncher.control_port to a new ControlPort (eg. 9052 for Tor Browser 2)
Edit TorButton Preferences (without the GUI [removed in 4.5 update])
Modify extensions.torbutton.custom.socks_port to a new port (eg. 9152 for Tor Browser 2)
Modify extensions.torbutton.custom.socks_host to 127.0.0.1
Modify extensions.torbutton.proxies_applied to false
Modify extensions.torbutton.use_privoxy to false
Modify network.proxy.socks_port to the same port (eg. 9152 for Tor Browser 2)
Close Tor Browser
Edit torrc-defaults in \TorBrowser\Data\Tor
Change SocksPort to what you set in step 5
Change ControlPort to what you set in step 4
Launch Tor Browser, and check that everything was configured correctly
Homepage (about:tor) should say "Congratulations!"
Click "Test Tor Network Settings". check.torproject.org should say "Congratulations."
Go to ip-check.info. Test should be all green and orange except Tab name. Authentication should be "protected". Note: It may not say that you are using Tor, but this is incorrect.