An internal login confirmation page for a site i wanted to use as an application in Fluid kept opening in a new tab in my default browser.
This seemed an extreme limitation so i started clicking through the preferences. Under Advanced Preferences i found "Allow browsing to URLs matching these patterns" and edited it to allow the entire site.
The problem had been that i made the application go to a specific page of the site as the starting page, and Fluid had used that to make its allowed pages rule.