I have no idea how this happened. I had my main domain.com up and running for almost a year and just recently added sub.domain.com ... both were running fine for a few days until I decided to add an SSL cert to www.domain.com to get rid of an 'insecure content' error. Everything now redirects to sub.domain.com I added the subdomain by adding a new website. I didn't use the subdomain or alias methods. If I deactivate sub.domain.com through ispconfig, I have access to www.domain.com again. I am using a wordpress installation for both domain.com and sub.domain.com and wordpress is set to use https://www.domain.com and https://sub.domain.com as the addresses for the sites. Where to start?
Check the ip addresses of the two websites, you probably have an ip address under sub.domain.com and '*' for the address under www.domain.com. Just set them both to the same thing (probably '*').
Okay it turns out it was the fact that I was using an old SSL cert that I had generated a while back. I had probably used domain.com and not domain.com plus www.domain.com Apache didn't like the cert. Made a new one and everything works just fine now.