After changing the setting to force 775 on directories and 644 on files the auto installer seemed to work but, ffmpeg is now left behind with 644 permissions. So the auto installer in my eyes is sort of useless if the client has to go and changes permissions. To that if they could or knew how to change permissions there would not be a need for an auto installer.

Also on my test server the cron job was not created as it should have been. The email did get sent out telling me what the cron path see more was so i suppose i could have put it in the cron tab myself.

Just my two cents and findings about the hype of the auto installer.