diff --git a/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java b/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
index 7353305f1..b12ae8e75 100644
--- a/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
+++ b/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
@@ -375,13 +375,14 @@ class RodBindingArgumentTypeDescriptor extends ArgumentTypeDescriptor {
                         if ( featureDescriptor != null ) {
                             tribbleType = featureDescriptor.getName();
                             logger.warn("Dynamically determined type of " + file + " to be " + tribbleType);
-                        } else {
-                            throw new UserException.CommandLineException(
-                                    String.format("No tribble type was provided on the command line and the type of the file could not be determined dynamically. " +
-                                            "Please add an explicit type tag :NAME listing the correct type from among the supported types:%n%s",
-                                            manager.userFriendlyListOfAvailableFeatures(parameterType)));
                         }
                     }
+
+                    if ( tribbleType == null )
+                        throw new UserException.CommandLineException(
+                                String.format("No tribble type was provided on the command line and the type of the file could not be determined dynamically. " +
+                                        "Please add an explicit type tag :NAME listing the correct type from among the supported types:%n%s",
+                                        manager.userFriendlyListOfAvailableFeatures(parameterType)));
                 }
             }
 
diff --git a/public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java b/public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java
index 12b454f4f..fbf8c6516 100755
--- a/public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java
+++ b/public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java
@@ -451,7 +451,7 @@ public class ParsingEngine {
      * @return A map of sources associated with this object and its aggregated objects and bindings to their bindings values
      */
     private Map<ArgumentSource, Object> extractArgumentBindings(Object obj, Class sourceClass, Field[] parentFields) {
-        Map<ArgumentSource, Object> bindings = new TreeMap<ArgumentSource, Object>();
+        Map<ArgumentSource, Object> bindings = new LinkedHashMap<ArgumentSource, Object>();
 
         while( sourceClass != null ) {
             Field[] fields = sourceClass.getDeclaredFields();
diff --git a/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java b/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
index fe08e5979..ff57bb744 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
@@ -120,7 +120,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
         args.put("hidden", new ArrayList<Object>());
         args.put("depreciated", new ArrayList<Object>());
         try {
-            for ( ArgumentSource argumentSource : parsingEngine.extractArgumentSources(HelpUtils.getClassForDoc(classdoc)) ) {
+            for ( ArgumentSource argumentSource : new TreeSet<ArgumentSource>(parsingEngine.extractArgumentSources(HelpUtils.getClassForDoc(classdoc))) ) {
                 ArgumentDefinition argDef = argumentSource.createArgumentDefinitions().get(0);
                 FieldDoc fieldDoc = getFieldDoc(classdoc, argumentSource.field.getName());
                 Map<String, Object> argBindings = docForArgument(fieldDoc, argumentSource, argDef); // todo -- why can you have multiple ones?