This is an update on issue #1800. This is SideKick 1.8 on jEdit stable 5.2.0 or trunk SVN 24023, on Linux.
Similar to #1800, the positioning of the popup menu does not work together with the scrollbar in the tree view, the main difference is that the popup stays within the height of the main jEdit view. Screenshot for SideKick + LaTeX tools is included.
Could you attach your test file? What look and feel are you using? I've tried a number of files and several look and feels, and cannot reproduce this problem.