Index: lams_central/src/java/org/lamsfoundation/lams/authoring/service/AuthoringService.java
===================================================================
diff -u -r57589d9a2eb658f07e1769b487bd47a4eb147673 -r21c2c5458bc48ec75db4e917444cca70448b4dea
--- lams_central/src/java/org/lamsfoundation/lams/authoring/service/AuthoringService.java	(.../AuthoringService.java)	(revision 57589d9a2eb658f07e1769b487bd47a4eb147673)
+++ lams_central/src/java/org/lamsfoundation/lams/authoring/service/AuthoringService.java	(.../AuthoringService.java)	(revision 21c2c5458bc48ec75db4e917444cca70448b4dea)
@@ -930,19 +930,33 @@
     			SequenceActivity newSequenceActivity = (SequenceActivity) activity;
             	// Need to check if the sets are not null as these are new objects and Hibernate may not have backed them with collections yet.
 	    		if ( newSequenceActivity.getBranchEntries() != null && newSequenceActivity.getBranchEntries().size() > 0 ) {
-	    			Iterator beIter = newSequenceActivity.getBranchEntries().iterator();
-	    			while ( beIter.hasNext() ) {
-	    				// sequence activity will be correct but the branching activity and the grouping will be wrong
-	    				// the condition was copied by the sequence activity copy
-	    				BranchActivityEntry entry = (BranchActivityEntry) beIter.next();
-	    				BranchingActivity oldBranchingActivity = entry.getBranchingActivity();
-	    				entry.setBranchingActivity((BranchingActivity) newActivities.get(LearningDesign.addOffset(oldBranchingActivity.getActivityUIID(), uiidOffset)));
-	    				Group oldGroup = entry.getGroup();
-	    				if ( oldGroup != null ) {
-	    					Grouping oldGrouping = oldGroup.getGrouping();
-	    					Grouping newGroouping = newGroupings.get(LearningDesign.addOffset(oldGrouping.getGroupingUIID(), uiidOffset));
-	    					entry.setGroup(newGroouping.getGroup(LearningDesign.addOffset(oldGroup.getGroupUIID(), uiidOffset)));
-	    				}
+	    			
+	    			Activity parentActivity = newSequenceActivity.getParentActivity();
+	    			if ( parentActivity.isChosenBranchingActivity() || 
+	    					( parentActivity.isGroupBranchingActivity() && parentActivity.getDefineLater()!=null &&
+	    					  parentActivity.getDefineLater().booleanValue())) {
+	    				// Don't have any preset up entries for a teacher chosen or a define later group based branching.
+	    				// Must be copying a design that was run previously.
+	    				newSequenceActivity.getBranchEntries().clear();
+
+	    			} else {
+		    			Iterator beIter = newSequenceActivity.getBranchEntries().iterator();
+		    			while ( beIter.hasNext() ) {
+		    				// sequence activity will be correct but the branching activity and the grouping will be wrong
+		    				// the condition was copied by the sequence activity copy
+		    				BranchActivityEntry entry = (BranchActivityEntry) beIter.next();
+		    				BranchingActivity oldBranchingActivity = entry.getBranchingActivity();
+		    				entry.setBranchingActivity((BranchingActivity) newActivities.get(LearningDesign.addOffset(oldBranchingActivity.getActivityUIID(), uiidOffset)));
+		    				Group oldGroup = entry.getGroup();
+		    				if ( oldGroup != null ) {
+		    					Grouping oldGrouping = oldGroup.getGrouping();
+		    					Grouping newGrouping = newGroupings.get(LearningDesign.addOffset(oldGrouping.getGroupingUIID(), uiidOffset));
+		    					if ( newGrouping != null ) {
+		    						entry.setGroup(newGrouping.getGroup(LearningDesign.addOffset(oldGroup.getGroupUIID(), uiidOffset)));
+		    					}
+		    				}
+		    			}
+	    				
 	    			}
 	    		}
     		}
Index: lams_common/src/java/org/lamsfoundation/lams/learningdesign/ChosenBranchingActivity.java
===================================================================
diff -u -r309a597eada52a4079f2985e0d97beedf9adda42 -r21c2c5458bc48ec75db4e917444cca70448b4dea
--- lams_common/src/java/org/lamsfoundation/lams/learningdesign/ChosenBranchingActivity.java	(.../ChosenBranchingActivity.java)	(revision 309a597eada52a4079f2985e0d97beedf9adda42)
+++ lams_common/src/java/org/lamsfoundation/lams/learningdesign/ChosenBranchingActivity.java	(.../ChosenBranchingActivity.java)	(revision 21c2c5458bc48ec75db4e917444cca70448b4dea)
@@ -136,6 +136,14 @@
     	ChosenBranchingActivity newBranchingActivity = new ChosenBranchingActivity();
     	copyBranchingFields(newBranchingActivity);
     	copyToNewComplexActivity(newBranchingActivity, uiidOffset);
+
+    	// Any grouping attached to a teacher chosen branching was either a runtime grouping
+    	// because we are running a runtime copy of a design, or some rubbish left from a bug in authoring.
+    	// We won't actually want this group, so remove references to it and they will be set up 
+    	// again when a lesson is started. 
+    	newBranchingActivity.setGrouping(null);
+    	newBranchingActivity.setGroupingUIID(null);
+    	newBranchingActivity.setApplyGrouping(false);
     	
     	return newBranchingActivity;
     }
Index: lams_common/src/java/org/lamsfoundation/lams/learningdesign/ToolBranchingActivity.java
===================================================================
diff -u -rdff974ef2462e40cacf7f8c737fc6ec4bb501806 -r21c2c5458bc48ec75db4e917444cca70448b4dea
--- lams_common/src/java/org/lamsfoundation/lams/learningdesign/ToolBranchingActivity.java	(.../ToolBranchingActivity.java)	(revision dff974ef2462e40cacf7f8c737fc6ec4bb501806)
+++ lams_common/src/java/org/lamsfoundation/lams/learningdesign/ToolBranchingActivity.java	(.../ToolBranchingActivity.java)	(revision 21c2c5458bc48ec75db4e917444cca70448b4dea)
@@ -133,14 +133,23 @@
     }
 
     /**
-     * Makes a copy of the BranchingActivity for authoring, preview and monitoring enviornment 
+     * Makes a copy of the BranchingActivity for authoring, preview and monitoring environment 
      * @return BranchingActivity Returns a deep-copy of the originalActivity
      */
     public Activity createCopy(int uiidOffset){
     	
     	ToolBranchingActivity newBranchingActivity = new ToolBranchingActivity();
     	copyBranchingFields(newBranchingActivity);
     	copyToNewComplexActivity(newBranchingActivity, uiidOffset);
+    	
+    	// Any grouping attached to a teacher chosen branching was either a runtime grouping
+    	// because we are running a runtime copy of a design, or some rubbish left from a bug in authoring.
+    	// We won't actually want this group, so remove references to it and they will be set up 
+    	// again when a lesson is started. 
+    	newBranchingActivity.setGrouping(null);
+    	newBranchingActivity.setGroupingUIID(null);
+    	newBranchingActivity.setApplyGrouping(false);
+ 
     	return newBranchingActivity;
     }