Overwritten Archives?

So, I installed wordpress into the root of my domain. Good (well, almost good… for some reason the permalinks seem not to be working). Then I decided to set up another blog in the subdirectory /blog of my domain. It installed fine and looked great, but with one snag.

When I click on the archives buttons of my root blog, it shows the archives of my blog in /blog subdirectory.

I was unaware that the archives default to the base of the domain regardless of the subdirectory the blog is installed in. Any idea how I can separate the two and fix this?