FYI, I will apply these patches to branch and trunk, as discussed with 
Jean-Marc on bugzilla.

Jürgen
Index: src/frontends/qt2/QDocumentDialog.C
===================================================================
--- src/frontends/qt2/QDocumentDialog.C	(Revision 15297)
+++ src/frontends/qt2/QDocumentDialog.C	(Arbeitskopie)
@@ -390,7 +390,8 @@ void QDocumentDialog::updateNumbering()
 	QListViewItem * item = 0;
 	for ( ; cit != end ; ++cit) {
 		int const toclevel = (*cit)->toclevel;
-		if (toclevel != LyXLayout::NOT_IN_TOC) {
+		if (toclevel != LyXLayout::NOT_IN_TOC 
+		    && (*cit)->labeltype == LABEL_COUNTER) {
 			item = new QListViewItem(numberingModule->tocLV,
 						 item, qt_((*cit)->name()));
 			item->setText(1, (toclevel <= depth) ? yes : no);
Index: src/frontends/qt2/ui/NumberingModuleBase.ui
===================================================================
--- src/frontends/qt2/ui/NumberingModuleBase.ui	(Revision 15297)
+++ src/frontends/qt2/ui/NumberingModuleBase.ui	(Arbeitskopie)
@@ -13,7 +13,7 @@
         <rect>
             <x>0</x>
             <y>0</y>
-            <width>310</width>
+            <width>306</width>
             <height>323</height>
         </rect>
     </property>
@@ -185,11 +185,11 @@
             </property>
             <property stdset="1">
                 <name>vScrollBarMode</name>
-                <enum>AlwaysOff</enum>
+                <enum>Auto</enum>
             </property>
             <property stdset="1">
                 <name>hScrollBarMode</name>
-                <enum>AlwaysOff</enum>
+                <enum>Auto</enum>
             </property>
             <property stdset="1">
                 <name>rootIsDecorated</name>
Index: src/frontends/qt3/QDocumentDialog.C
===================================================================
--- src/frontends/qt3/QDocumentDialog.C	(Revision 15350)
+++ src/frontends/qt3/QDocumentDialog.C	(Arbeitskopie)
@@ -436,7 +436,8 @@ void QDocumentDialog::updateNumbering()
 	QListViewItem * item = 0;
 	for ( ; cit != end ; ++cit) {
 		int const toclevel = (*cit)->toclevel;
-		if (toclevel != LyXLayout::NOT_IN_TOC) {
+		if (toclevel != LyXLayout::NOT_IN_TOC 
+		    && (*cit)->labeltype == LABEL_COUNTER) {
 			item = new QListViewItem(numberingModule->tocLV,
 						 item, qt_((*cit)->name()));
 			item->setText(1, (toclevel <= depth) ? yes : no);
Index: src/frontends/qt3/ui/NumberingModuleBase.ui
===================================================================
--- src/frontends/qt3/ui/NumberingModuleBase.ui	(Revision 15350)
+++ src/frontends/qt3/ui/NumberingModuleBase.ui	(Arbeitskopie)
@@ -144,10 +144,10 @@
                 <enum>AutoOneFit</enum>
             </property>
             <property name="vScrollBarMode">
-                <enum>AlwaysOff</enum>
+                <enum>Auto</enum>
             </property>
             <property name="hScrollBarMode">
-                <enum>AlwaysOff</enum>
+                <enum>Auto</enum>
             </property>
             <property name="rootIsDecorated">
                 <bool>false</bool>
Index: src/frontends/qt4/QDocumentDialog.C
===================================================================
--- src/frontends/qt4/QDocumentDialog.C	(Revision 15350)
+++ src/frontends/qt4/QDocumentDialog.C	(Arbeitskopie)
@@ -622,7 +622,8 @@ void QDocumentDialog::updateNumbering()
 	QTreeWidgetItem * item = 0;
 	for ( ; cit != end ; ++cit) {
 		int const toclevel = (*cit)->toclevel;
-		if (toclevel != LyXLayout::NOT_IN_TOC) {
+		if (toclevel != LyXLayout::NOT_IN_TOC 
+		    && (*cit)->labeltype == LABEL_COUNTER) {
 			item = new QTreeWidgetItem(numberingModule->tocTW);
 			item->setText(0, qt_((*cit)->name()));
 			item->setText(1, (toclevel <= depth) ? yes : no);

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