Thank you for writing.
Could you give us more details on how are you setting the padding - at design time, run time, or through custom theme? I set the top padding at design time and everything worked fine, also if you set the treeview height to some value, and you set enough top padding, the tree nodes at the bottom will disappear, which is normal.
Can you send us a sample application, so that we can assist you further. Please open a new support ticket so that you can attach files. Thank you in advance.
the Telerik team