RegisterStartupScript doesn't work with ScriptManager,Updatepanel. Why is that?

protected void timer1_Tick(object sender, EventArgs e)
    {
        foreach (RepeaterItem item in rpChat.Items)
        {
            TextBox txt = item.FindControl("txtChatMessage") as TextBox;
            if (txt != null)
            {
                message[i] = txt.Text;
                i--;
            }
        }
        lblStatusChat.Text = "";
        RepeaterBind();
        string javaScript = "<script language=JavaScript>\n" + "alert('Button1_Click client-side');\n" + "</script>";

        Page.ClientScript.RegisterStartupScript(this.GetType(), "myKey", javaScript);
    }

timer_click trigggers and update panel. And the alert message doesnt show up on timer_tick event

When you use an UpdatePanel, then you can not call JavaScript using ClientScript as you have tried to. You have to use ScriptManager.RegisterStartupScript instead.

So change your

Page.ClientScript.RegisterStartupScript(this.GetType(), "myKey", javaScript);

to

ScriptManager.RegisterStartupScript(updatePanelId,updatePanelId.GetType(), "alert", javaScript, true);

You need to user ScriptManager class because you are register script when doing postback and using updatepanel

MSDN: ScriptManager.RegisterStartupScript

ScriptManager.RegisterStartupScript method used to add client script to a page when the control is wrapped inside an UpdatePanel.

ASPX page

<div>
<asp:ScriptManager ID="ScriptManager1" runat="server">
</asp:ScriptManager>
<asp:UpdatePanel ID="UpdatePanel1" runat="server">
    <ContentTemplate>
        <asp:Label ID="lblDisplayDate" runat="server" Text="Label"></asp:Label>
         <asp:Button ID="btnPostback" runat="server" onclick="btnPostback_Click" 
        Text="ClickMe" />
    </ContentTemplate>
</asp:UpdatePanel>
</div>

CodeBehind Register StartUp Script

protected void btnPostback_Click(object sender, EventArgs e)
{
    System.Text.StringBuilder sb = new System.Text.StringBuilder();
    sb.Append(@"<script language='javascript'>");
    sb.Append(@"var lbl = document.getElementById('lblDisplayDate');");
    sb.Append(@"lbl.style.color='red';");
    sb.Append(@"</script>");

    ScriptManager.RegisterStartupScript(btnPostback,this.GetType(), "JSCR", sb.ToString(),false);

}

Detail : Add JavaScript programmatically using RegisterStartupScript during an Asynchronous postback

In my case ScriptManager.RegisterStartupScript didn't work too.

Not work:

ScriptManager.RegisterStartupScript(Me, 
  Me.GetType(), 
  String.Format("Data{0}", Me.ID), 
  "<script>alert(111);</script>", 
  False)

Work:

ScriptManager.RegisterStartupScript(Me.Page, 
  Me.GetType(), 
  String.Format("Data{0}", Me.ID), 
  "<script>alert(111);</script>", 
  False)

Me in the example is my custom control inherited from System.Web.UI.WebControls.WebParts.WebPart