FULL PRODUCT VERSION :
java version "1.6.0"
Java(TM) SE Runtime Environment (build 1.6.0-b105)
Java HotSpot(TM) Client VM (build 1.6.0-b105, mixed mode, sharing)


ADDITIONAL OS VERSION INFORMATION :
Microsoft Windows XP [Version 5.1.2600]

A DESCRIPTION OF THE PROBLEM :
javax.swing.tree.VariableHeightLayoutCache skips updateYLocationsFrom() when evaluating children of an invisible root.

VariableHeightLayoutCache contains the following code

public void treeNodesChanged(TreeModelEvent e) {
    if(e != null) {
. . .
changedNode = getNodeForPath(e.getTreePath(), false, false);
. . .
if(!isFixedRowHeight()) {
int aRow = changedNode.getRow();

if(aRow != -1)
this.updateYLocationsFrom(aRow);
}
. . .
    }
}

e.getTreePath() points to the parent of the nodes that were changed.

If said parent is the root, and setRootVisible()==false, then changedNode will not be in the visibleNodes Vector, and thus aRow will be set to -1.

This means that row height changes to top level nodes in a JTree will not change the Y-offsets of nodes that follow them. This is bad (tm).

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
The same result as when s has the initial value "Two\nThree"
ACTUAL -
One
Two
Three
Five
Six
(with Four occasionally displacing Three)
Also, odd behaviour when selecting nodes.

REPRODUCIBILITY :
This bug can be reproduced always.

---------- BEGIN SOURCE ----------

import java.awt.*;
import javax.swing.*;
import javax.swing.tree.*;

public class TreeTest {

    static class ComponentCellRenderer extends JTextArea implements TreeCellRenderer {
        public Component getTreeCellRendererComponent(JTree tree, Object value, boolean selected, boolean expanded,
                boolean leaf, int row, boolean hasFocus) {
            setText(value.toString());
            if (selected) setForeground(selectionForeground);
            else setForeground(textForeground);
            if (selected) setBackground(selectionBackground);
            else setBackground(textBackground);
            return this;
        }
    }

    static String s = "Two-Three";
    static Color selectionForeground = UIManager.getColor("Tree.selectionForeground");
    static Color textForeground = UIManager.getColor("Tree.textForeground");
    static Color selectionBackground = UIManager.getColor("Tree.selectionBackground");
    static Color textBackground = UIManager.getColor("Tree.textBackground");

    public static void main(String[] args) {
        JFrame f = new JFrame();

        Object relay = new Object() {public String toString() {return s;}};
        JTree tree = new JTree(new Object[]{"One", relay, "Four", "Five", "Six"});
        tree.setCellRenderer(new ComponentCellRenderer());
        f.add(tree);
        f.pack();
        f.setVisible(true);
        s = "Two\nThree";
        DefaultTreeModel model = (DefaultTreeModel) tree.getModel();
        DefaultMutableTreeNode root = (DefaultMutableTreeNode) model.getRoot();
        model.nodeChanged(root.getChildAt(1));
    }
}
---------- END SOURCE ----------

CUSTOMER SUBMITTED WORKAROUND :
Manually calling treeState.invalidatePathBounds(tree.getPathForRow(0)); when appropriate. Note that it has to go rather late in the sequence, because other wise the height change won't have happened yet.