I had an issue using this in a user control (in a page this worked fine); the Button1 is inside an updatepanel, and the scriptmanager is on the usercontrol.
protected void Button1_Click(object sender, EventArgs e)
{
string scriptstring = "alert('Welcome');";
ScriptManager.RegisterStartupScript(this, this.GetType(), "alertscript", scriptstring, true);
}
Now it seems you have to be careful with the first two arguments, they need to reference your page, not your control
ScriptManager.RegisterStartupScript(this.Page, this.Page.GetType(), "alertscript", scriptstring, true);