Currently this cluster I'm working on has 3 sites on it, they are separate entities, however and not part of a multisite. Site 1 at http://www.domain.com acts as a landing page for sites 2 at http://www.domain.com/site1 and site 3 at http://www.domain.com/site2.
I attempted to use a cache plugin on one of the second level sites (Hyper Cache). I deactivated and deleted that plugin as well as went into my FTP client to ensure everything was cleared out. The problem I have now is on my second level site, the homepage appears fine, wp-admin works and has full functionality, I can view and edit all my pages in wp-admin, but when I navigate to any of the other pages on the site it displays the correct address but is really trying to pull the pages from the top level (splash) site where they do not exist and I'm getting 404 errors.
So essentially http://www.domain.com/site2/page is a page on site 2, but instead it's trying to find/site2/page on the actual http://www.domain.com site. The 404 error shows on the http://www.domain.com site.
I tried taking a fresh copy of the .htaccess file I had from an older backup as well as a fresh wp-config file onto the /site2 site. The other website (www.domain.com/site1) works normally, so I'm going to rule that it was an issue caused by the cache plugin, but I don't know where the mistake would be so it can be corrected.
Any assistance is appreciated.