Since GTK+ 2.18 has introduced Client Side Windows, a couple of problems have appeared in Eclipse 3.5. One of them was resolved in GTK+ 2.18.0 (https://bugzilla.gnome.org/show_bug.cgi?id=589963), the other one needs fixing at the SWT-level (https://bugs.eclipse.org/bugs/show_bug.cgi?id=287307)

Since I don’t want to run Eclipse 3.6 milestones yet, I created a small diff between the two SWT versions (3.5.1 and 3.6) and isolated the necessary changes. I am currently running Eclipse 3.5.1 with this patch on my Ubuntu Karmic installation, and it fixes the problem.

Here is the diff:
diff -urN swt-3.5/org/eclipse/swt/internal/gtk/OS.java swt-3.6/org/eclipse/swt/internal/gtk/OS.java
— swt-3.5/org/eclipse/swt/internal/gtk/OS.java    2009-08-20 15:16:38.000000000 +0200
+++ swt-3.6/org/eclipse/swt/internal/gtk/OS.java    2009-09-17 05:24:42.000000000 +0200
@@ -4887,6 +4885,21 @@
lock.unlock();
}
}
+/**
+ * @method flags=dynamic
+ * @param window cast=(GdkWindow *)
+ * @param sibling cast=(GdkWindow *)
+ * @param above cast=(gboolean)
+ */
+public static final native void _gdk_window_restack(int /*long*/ window, int /*long*/ sibling, boolean above);
+public static final void gdk_window_restack(int /*long*/ window, int /*long*/ sibling, boolean above) {
+    lock.lock();
+    try {
+        _gdk_window_restack(window, sibling, above);
+    } finally {
+        lock.unlock();
+    }
+}
/** @param window cast=(GdkWindow *) */
public static final native void _gdk_window_scroll(int /*long*/ window, int dx, int dy);
public static final void gdk_window_scroll(int /*long*/ window, int dx, int dy) {
diff -urN swt-3.5/org/eclipse/swt/widgets/Control.java swt-3.6/org/eclipse/swt/widgets/Control.java
— swt-3.5/org/eclipse/swt/widgets/Control.java    2009-08-07 14:50:38.000000000 +0200
+++ swt-3.6/org/eclipse/swt/widgets/Control.java    2009-09-17 05:24:42.000000000 +0200
@@ -3332,6 +3319,30 @@
region = null;
}

+void restackWindow (int /*long*/ window, int /*long*/ sibling, boolean above) {
+        if (OS.GTK_VERSION >= OS.VERSION (2, 17, 11)) {
+            OS.gdk_window_restack (window, sibling, above);
+        } else {
+            /*
+            * Feature in X. If the receiver is a top level, XConfigureWindow ()
+            * will fail (with a BadMatch error) for top level shells because top
+            * level shells are reparented by the window manager and do not share
+            * the same X window parent.  This is the correct behavior but it is
+            * unexpected.  The fix is to use XReconfigureWMWindow () instead.
+            * When the receiver is not a top level shell, XReconfigureWMWindow ()
+            * behaves the same as XConfigureWindow ().
+            */
+            int /*long*/ xDisplay = OS.gdk_x11_drawable_get_xdisplay (window);
+            int /*long*/ xWindow = OS.gdk_x11_drawable_get_xid (window);
+            int xScreen = OS.XDefaultScreen (xDisplay);
+            int flags = OS.CWStackMode | OS.CWSibling;
+            XWindowChanges changes = new XWindowChanges ();
+            changes.sibling = OS.gdk_x11_drawable_get_xid (sibling);
+            changes.stack_mode = above ? OS.Above : OS.Below;
+            OS.XReconfigureWMWindow (xDisplay, xWindow, xScreen, flags, changes);
+        }
+    }
+
boolean sendDragEvent (int button, int stateMask, int x, int y, boolean isStateMask) {
Event event = new Event ();
event.button = button;
@@ -3682,15 +3693,7 @@
if (!OS.GDK_WINDOWING_X11 ()) {
OS.gdk_window_raise (enableWindow);
} else {
–                int /*long*/ topWindow = OS.GTK_WIDGET_WINDOW (topHandle);
–                int /*long*/ xDisplay = OS.gdk_x11_drawable_get_xdisplay (topWindow);
–                int /*long*/ xWindow = OS.gdk_x11_drawable_get_xid (enableWindow);
–                int xScreen = OS.XDefaultScreen (xDisplay);
–                int flags = OS.CWStackMode | OS.CWSibling;
–                XWindowChanges changes = new XWindowChanges ();
–                changes.sibling = OS.gdk_x11_drawable_get_xid (topWindow);
–                changes.stack_mode = OS.Above;
–                OS.XReconfigureWMWindow (xDisplay, xWindow, xScreen, flags, changes);
+                restackWindow (enableWindow, OS.GTK_WIDGET_WINDOW (topHandle), true);
}
if (OS.GTK_WIDGET_VISIBLE (topHandle)) OS.gdk_window_show_unraised (enableWindow);
}
@@ -4170,29 +4173,12 @@
OS.gdk_window_lower (window);
}
} else {
–            XWindowChanges changes = new XWindowChanges ();
–            changes.sibling = OS.gdk_x11_drawable_get_xid (siblingWindow != 0 ? siblingWindow : redrawWindow);
–            changes.stack_mode = above ? OS.Above : OS.Below;
–            if (redrawWindow != 0 && siblingWindow == 0) changes.stack_mode = OS.Below;
–            int /*long*/ xDisplay = OS.gdk_x11_drawable_get_xdisplay (window);
–            int /*long*/ xWindow = OS.gdk_x11_drawable_get_xid (window);
–            int xScreen = OS.XDefaultScreen (xDisplay);
–            int flags = OS.CWStackMode | OS.CWSibling;
–            /*
–            * Feature in X. If the receiver is a top level, XConfigureWindow ()
–            * will fail (with a BadMatch error) for top level shells because top
–            * level shells are reparented by the window manager and do not share
–            * the same X window parent.  This is the correct behavior but it is
–            * unexpected.  The fix is to use XReconfigureWMWindow () instead.
–            * When the receiver is not a top level shell, XReconfigureWMWindow ()
–            * behaves the same as XConfigureWindow ().
–            */
–            OS.XReconfigureWMWindow (xDisplay, xWindow, xScreen, flags, changes);
+            int /*long*/ siblingW = siblingWindow != 0 ? siblingWindow : redrawWindow;
+            boolean stack_mode = above;
+            if (redrawWindow != 0 && siblingWindow == 0) stack_mode = false;
+            restackWindow (window, siblingW, stack_mode);
if (enableWindow != 0) {
–                changes.sibling = OS.gdk_x11_drawable_get_xid (window);
–                changes.stack_mode = OS.Above;
–                xWindow = OS.gdk_x11_drawable_get_xid (enableWindow);
–                OS.XReconfigureWMWindow (xDisplay, xWindow, xScreen, flags, changes);
+                 restackWindow (enableWindow, window, true);
}
}
}
diff -urN swt-3.5/os.c swt-3.6/os.c
— swt-3.5/os.c    2009-05-29 17:30:14.000000000 +0200
+++ swt-3.6/os.c    2009-09-17 05:24:42.000000000 +0200
@@ -5944,6 +5932,24 @@
}
#endif

+#ifndef NO__1gdk_1window_1restack
+JNIEXPORT void JNICALL OS_NATIVE(_1gdk_1window_1restack)
+    (JNIEnv *env, jclass that, jintLong arg0, jintLong arg1, jboolean arg2)
+{
+    OS_NATIVE_ENTER(env, that, _1gdk_1window_1restack_FUNC);
+/*
+    gdk_window_restack((GdkWindow *)arg0, (GdkWindow *)arg1, (gboolean)arg2);
+*/
+    {
+        LOAD_FUNCTION(fp, gdk_window_restack)
+        if (fp) {
+            ((void (CALLING_CONVENTION*)(GdkWindow *, GdkWindow *, gboolean))fp)((GdkWindow *)arg0, (GdkWindow *)arg1, (gboolean)arg2);
+        }
+    }
+    OS_NATIVE_EXIT(env, that, _1gdk_1window_1restack_FUNC);
+}
+#endif
+
#ifndef NO__1gdk_1window_1scroll
JNIEXPORT void JNICALL OS_NATIVE(_1gdk_1window_1scroll)
(JNIEnv *env, jclass that, jintLong arg0, jint arg1, jint arg2)
diff -urN swt-3.5/os_custom.h swt-3.6/os_custom.h
— swt-3.5/os_custom.h    2009-05-29 17:30:14.000000000 +0200
+++ swt-3.6/os_custom.h    2009-09-17 05:24:42.000000000 +0200
@@ -112,6 +113,7 @@
#define gtk_status_icon_set_tooltip_LIB “libgtk-x11-2.0.so.0”
#define gtk_window_get_group_LIB “libgtk-x11-2.0.so.0”
#define gtk_window_get_opacity_LIB “libgtk-x11-2.0.so.0”
+#define gdk_window_restack_LIB “libgdk-x11-2.0.so.0”
#define gdk_window_set_keep_above_LIB “libgdk-x11-2.0.so.0”
#define gdk_window_set_accept_focus_LIB “libgdk-x11-2.0.so.0”
#define gtk_window_set_opacity_LIB “libgtk-x11-2.0.so.0”
diff -urN swt-3.5/os_stats.c swt-3.6/os_stats.c
— swt-3.5/os_stats.c    2009-05-29 17:30:14.000000000 +0200
+++ swt-3.6/os_stats.c    2009-09-17 05:24:42.000000000 +0200
@@ -18,8 +18,8 @@

#ifdef NATIVE_STATS

-int OS_nativeFunctionCount = 1291;
-int OS_nativeFunctionCallCount[1291];
+int OS_nativeFunctionCount = 1292;
+int OS_nativeFunctionCallCount[1292];
char * OS_nativeFunctionNames[] = {
#ifndef JNI64
“Call__IIII”,
@@ -503,6 +502,7 @@
“_1gdk_1window_1raise”,
“_1gdk_1window_1remove_1filter”,
“_1gdk_1window_1resize”,
+    “_1gdk_1window_1restack”,
“_1gdk_1window_1scroll”,
“_1gdk_1window_1set_1accept_1focus”,
“_1gdk_1window_1set_1back_1pixmap”,
diff -urN swt-3.5/os_stats.h swt-3.6/os_stats.h
— swt-3.5/os_stats.h    2009-05-29 17:30:14.000000000 +0200
+++ swt-3.6/os_stats.h    2009-09-17 05:24:42.000000000 +0200
@@ -511,6 +510,7 @@
_1gdk_1window_1raise_FUNC,
_1gdk_1window_1remove_1filter_FUNC,
_1gdk_1window_1resize_FUNC,
+    _1gdk_1window_1restack_FUNC,
_1gdk_1window_1scroll_FUNC,
_1gdk_1window_1set_1accept_1focus_FUNC,
_1gdk_1window_1set_1back_1pixmap_FUNC,