So I ran the auto installer and my S3 went through the process and successfully installed CM onto my phone. Where in the settings of the phone can I confirm that it's CM because when I pull down the settings menu it still looks like TW 4.3?
Ok, it does not show the CM boot sequence but I know the install completed. I guess I should try the manual install instead of the windows method via their website then.
Open Settings > about phone and check the build number. It should say CM and a build date.
With flashing have you done so manually through the recovery before or is this your first time and are using the installer? I have not used the installer and wouldn't know where to begin with troubleshooting. If you can do it manually give it a try and see if you have success.