I've installed my WP in a subdirectory to keep it from being displayed on the root until I was finished spiffing it up.
It just went live yesterday, and I set the site address as the root URL and the WP address as the directory to keep things clean, going through all the hoops. No problems now, and http://mysite.com displays the WP installation perfectly.
However, I have another unrelated folder of http://mysite.com/slide/ which has a web-based comic reading program installed. It shows up fine, but any directories beyond it, like http://mysite.com/slide/reader/chapter_1, WP tries to read as WP entries and displays a 404 page from the blog, which isn't even related to it.
Please help? I've tried changing permalink settings, to no avail.