Ok...you're using the timer and thus asp.net AJAX. You can't (and NEVER should for registering js) use Response.Write. Do this:
ClientScript.RegisterClientScriptBlock(TypeOf(Page), "unique_key" & DateTime.Now, "window.open('', '_parent', '');", True)
If you wish to have the script loaded only once, make the second param constant (that is, remove the DateTime.Now).