Well, I don't know what to say. The popup window does not have an instance of CuteEditor. I happen to have Editor.Focus = False  on my page load for both of my CuteEditor instances. I've tried the following two methods to open a popup window;

1) RegisterClientScriptBlock("clientScript", "<script language=""javascript"">var w=window.open('AddLinks.aspx?id=" & intID & "'); w.self.focus();</script>") 
2) RegisterClientScriptBlock("clientScript", "<script language=""javascript"">window.open('AddLinks.aspx?id=" & intID & "');</script>").

They both popup fine, but then dissapear under the previous window with the CuteEditor instances. And while it doesn't seem either CuteEditor instance has focus, this behaviour started when I upgraded from the last 4.0.0.x version to 4.5.0.1.