Hello! StartupPath not work. 
I downloaded latest version CKFinder for asp.net, created simple project. (WebSite1)
I tested in VS 2010 Express, framework 4.0
I set in config.ascx
// The base URL used to reach files in CKFinder through the browser.
BaseUrl = "/WebSite1/ckfinder/userfiles/";
BaseDir = "";
aspx page:
<%@ Page Language="C#" AutoEventWireup="true" CodeFile="Default.aspx.cs" Inherits="_Default" %> <%@ Register Assembly="CKFinder" Namespace="CKFinder" TagPrefix="CKFinder" %> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml"> <head runat="server"> <title></title> </head> <body> <form id="form1" runat="server"> <div> <CKFinder:FileBrowser ID="FB_Gallery" BasePath="/WebSite1/ckfinder/" Width="800" runat="server" ></CKFinder:FileBrowser> </div> </form> </body> </html>