I’ve actually been having the same problem with GoDaddy. They told me to go into domain management and give my additional website its own folder. But they didn’t say which folder to assign it to. Do you remember which folder you assigned your second site to?
I thought I was suposed to assign it to blogs.dir, however it kept giving me an error msg. It said the folder I choose cannot have a period in it.
Any help at all will be greatly appreciated