Calling setBackground() on a JTree changes the color of the tree spinner, not the tree, on GTK L&F. While NetBeans is not directly impacted by this, other apps may be, so probably this should be fixed along with the rest of the background color issues.
See attached demo app (a NetBeans project - unzip and run "ant run" to build and run it) - it will show a frame, then on a timer, set the colors of all components in the frame, then do so again, also setting the selected state of all AbstractButtons in the frame.
(This issue originally intended to be part of bug 4997237 which has been closed)