Ok here's what happened. When I started messing with the .vhost file I did this
cp mysite.org.vhost mysite.org.backup
I wasn't aware that .vhost file was overwritten by crons.
I also wasn't aware that apache would go straight for the file that said .backup instead of the one that said .vhost I suppose I was thinking the file extensions mattered. Bah!
Thanks for the help.