Apparently, the ordering of your <%@ Assembly %> directive before your <%@ Page %> in custom WSS application pages makes a difference. Make sure you put the Assembly directive before the Page directive:

<%@ Assembly Name="MyWebApp, Version=1.0.0.0, 
	Culture=neutral, PublicKeyToken=abcdefg817264759" %>
<%@ Page MasterPageFile="~/_layouts/application.master" Language="C#" 
	Inherits="MyWebApp.MyForm" %>

This is incorrect:

<!-- INCORRECT -->
<%@ Page MasterPageFile="~/_layouts/application.master" Language="C#"
	Inherits="MyWebApp.MyForm" %>
<%@ Assembly Name="MyWebApp, Version=1.0.0.0, 
	Culture=neutral, PublicKeyToken=abcdefg817264759" %>

Doing it the incorrect way, you'll get a generic error message:

This rule probably applies in other ASP .Net cases, but I've never come across it before.