I develop with 1.1 and 2.0 - When VS 2003 creates a web solution it is configured to use the 2.0 runtime. Placeing the following code to the Global.asax's of your 1.1 projects and setting execute permissions on the aspnet_regiis.exe helps much.
protected void Application_Start(Object sender, EventArgs e)
{
if(System.Environment.Version.Major==2)
{
System.Diagnostics.Process _p = new System.Diagnostics.Process();
_p.StartInfo.FileName = "%WINDIR%\\Microsoft.NET\\Framework\\v1.1.4322\\aspnet_regiis.exe";
_p.StartInfo.Arguments = "-s W3SVC/1/ROOT" + Request.ApplicationPath;
_p.StartInfo.UseShellExecute = false;
_p.StartInfo.RedirectStandardOutput = true;
_p.Start();
}
}