Let me start off by saying that I have reproduced this behaviour in the on-line samples (specifically the FlowCharter sample) using both IE 7.0 and FireFox 2.0.0.9
The context menu appears "higher" than the expected location when right-clicking a node if the page is scrolled.
Resize your browser window such that vertical scrollbar appears
Scroll-down enough to make the error obvious (2 inches at least)
Drop a node onto the GoView
Right-click the node
Presto - the context menu pops up but "higher" than its expected location
The lower you scroll the "higher" the context menu appears. It also seems to be approximately the same distance higher as you've scrolled down - it would seem (unconfirmed) that the popup is being positioned using view coordinates but on the page (where it should be using page coordinates).