http://wordpress.org/support/topic/156062 the guy who started this topic had the same exact issue I'm having, but I'll explain it just the same and see if anyone has any ideas or suggestions.
So I have a website, http://www.1stdomain.com, it's my main site and gets 95% of any traffic coming to the few sites I run. I have hosting setup for that site, but have made a few addon domains for the three other small sites I run. I'm not sure if the way my hosting company does it is normal or not, but say I setup http://www.2nddomain.com, a subdomain is created in my main domain. So 2nddomain.1stdomain.com or http://www.1stdomain.com/2nddomain would hold all the info for http://www.2nddomain.com. I'm pretty sure that's common practice.
So my issue is, I'm trying to create a site that city council members will see, parents, people who need to see a professional site. So I've bought a domain, http://www.bikejumps.info This will be where I send people when they ask for info. But my main site where everything is hosted (www.destroybmx.com) is not so "professional". With talk about hookers, people drinking 40's, whatever. I mean, nothing illegal, but nothing I want the mayor of our city to see when we're asking for a favor.
Here is the problem. I've been able to install WP into bikejumps.destroybmx.com When I go to http://www.bikejumps.info, it's there for me. But past that point, everything is http://www.destroybmx.com/bikejumps/...
Obviously, I need there to be no visible connection between the two sites. I've been trying to track this down for a few days now with no real idea of what to do. Like I said, that topic I put at the top of this one is the closest thing I could find. I've tried the canonical plugin, changing the permalinks, but it will not let me stay inside the http://www.bikejumps.info domain, it always has me at http://www.destroybmx.com/bikejumps/
So, after all that explanation so I can make it perfectly clear, what can I do outside of a whole new hosting package or dealing with it saying that?