Not sure what example you are trying, but here is what I did to try and reproduct your problem.
1) Download the source version of the webcontrol project here.
2) Create a new sub called test with your code in it.
Private Sub Test()
Me.MyDNNTree.PopulateNodesFromClient = True
Me.MyDNNTree.ForceDownLevel = False
Me.MyDNNTree.CheckBoxes = False
Me.MyDNNTree.JSFunction = "myTestFunction('TestParam1', 'TestParam2');"
Me.MyDNNTree.Target = "MyTarget"
MyDNNTree.IndentWidth = 20
MyDNNTree.TreeNodes.Clear()
Dim objNode As DotNetNuke.UI.WebControls.TreeNode = New DotNetNuke.UI.WebControls.TreeNode("root")
objNode.Key = "test1"
objNode.ToolTip = "Test2"
objNode.Text = "this is a thing"
MyDNNTree.TreeNodes.Add(objNode)
End Sub
3) Comment out the call to SetTreeDefaults() and call Test() in stead in Page_Load
'SetTreeDefaults()
Test()
4) Tested page. This code worked and showed your single node. The image was messed up, but I don't think that is your concern at the moment.
If you are still having trouble with this sample I think I may need some more info from you.