I have a VS 2005 web site that I publish using "Publish Web Site", and I clear all the three checkboxes. I also have a deployment project that picks up the published files and creates an MSI. I then install the package on a separate test server.
In other words, the whole site is pre-compiled. However, when I go to any .aspx file in a specific subfolder named "Services", I get an HttpException:
System.Web.HttpException: The file '/myapp/Services/mypage.aspx' has not been pre-compiled, and cannot be requested.
<%@ Page Language="C#" AutoEventWireup="true" CodeFile="mypage.aspx.cs" Inherits="Services_mypage" %>"
I've not had that error, but after a little Googling I came across this link, I'm not sure if you've seen it yet: http://forums.asp.net/t/956297.aspx
People were reporting that missing assemblies on the destination server ended up being the root cause, in their cases, but they had the same error as you. Weird.
Maybe that's the problem?