This adjustment has resolved it:

Public Class Form1
    Inherits Framework.Form

    Private Sub Form1_Load(ByVal sender As Object, ByVal e As System.EventArgs) Handles MyBase.Load

        ' Add a handler when the window will be minized
        AddHandler Resize, AddressOf MainForm_Minimize

        ' Add a handler for the notify icon MouseDown
        AddHandler NotifyIcon1.MouseDown, AddressOf NotifyIcon1_MouseDown

        ' Do not show this window in taskbar
        ShowInTaskbar = False

    End Sub

    Private Sub MainForm_Minimize(ByVal sender As Object, ByVal e As EventArgs)

        If WindowState = FormWindowState.Minimized Then
            NotifyIcon1.Visible = True
            NotifyIcon1.Text = "CCS Agent"
            Hide()
        End If

    End Sub

    Private Sub NotifyIcon1_MouseDown(ByVal sender As Object, ByVal e As MouseEventArgs)
        Show()
        NotifyIcon1.Visible = False
        WindowState = FormWindowState.Normal
        Focus()
    End Sub

End Class

I guess with the previous version, when ShowInTaskbar=False, the EXE will be forced to be shown in the lower left of the desktop. The Hide() command resolves the issue.