[Erel]

Here is a workaround for this issue (which is a .Net CF issue):
Make sure to use the updated ControlsEx library.

Sub Globals

End Sub

Sub App_Start
    Init
    FMain.Show
End Sub

Sub Init 
    Tree1.New1("FMain",5,5,230,230)
    Tree1.CheckBoxes = True
    node1.New1
    node1.Value = Tree1.AddNewNode("Node1")
    node1.Value = Tree1.AddNewNode("Node2")
    node1.Checked = True
End Sub

Sub BtnJump_Click
    node1.Value = Tree1.GetNode(1)
    Tree1.RemoveNodeAt(1)
    Tree1.InsertNode(0, node1.Value)
End Sub

Sub Tree1_AfterCheck
      If tree1.Action = "unknown" Then Return
      node1.Value = tree1.CheckedNode
      node1.Checked = node1.Checked
End Sub