The tree context menu goes to a strange position if a node has children nodes and they are open.
Here ares some screen shots to help you, on both I clicked the same node , the "TB_MOVIE" node..
Change the element you are aligning it to. node.ui.getAnchor() will position it under the node's text. You can also change where it aligns on the anchor by passing an alignment as the second param to show(). See Element.alignTo for more details.