diff --git a/jetty-start/src/main/java/org/eclipse/jetty/start/Modules.java b/jetty-start/src/main/java/org/eclipse/jetty/start/Modules.java
index f52bd049122..5224a00525c 100644
--- a/jetty-start/src/main/java/org/eclipse/jetty/start/Modules.java
+++ b/jetty-start/src/main/java/org/eclipse/jetty/start/Modules.java
@@ -271,9 +271,13 @@ public class Modules implements Iterable<Module>
         }
       
         // Enable the  module
-        if (module.enable(enabledFrom,transitive))
+        if (module.isEnabled() && !transitive)
         {
-            StartLog.debug("enabled %s",module.getName());
+            StartLog.info("Module %s has already been enabled.", module.getName());
+        }
+        else if (module.enable(enabledFrom,transitive))
+        {
+            StartLog.debug("Enabled %s",module.getName());
             newlyEnabled.add(module.getName());
             
             // Expand module properties
@@ -290,8 +294,7 @@ public class Modules implements Iterable<Module>
         }
         else if (module.isTransitive() && module.hasIniTemplate())
             newlyEnabled.add(module.getName());
-        
-        
+
         // Process module dependencies (always processed as may be dynamic)
         for(String dependsOn:module.getDepends())
         {
diff --git a/jetty-start/src/main/java/org/eclipse/jetty/start/builders/StartIniBuilder.java b/jetty-start/src/main/java/org/eclipse/jetty/start/builders/StartIniBuilder.java
index dbfdc209934..d3027489578 100644
--- a/jetty-start/src/main/java/org/eclipse/jetty/start/builders/StartIniBuilder.java
+++ b/jetty-start/src/main/java/org/eclipse/jetty/start/builders/StartIniBuilder.java
@@ -88,12 +88,6 @@ public class StartIniBuilder implements BaseBuilder.Config
     @Override
     public boolean addModule(Module module) throws IOException
     {
-        if (modulesPresent.contains(module.getName()))
-        {
-            StartLog.info("%-15s already initialised in %s",module.getName(),baseHome.toShortForm(startIni));
-            // skip, already present
-            return false;
-        }
 
         if (module.isDynamic())
         {
diff --git a/jetty-start/src/test/resources/usecases/alternate.5.assert.txt b/jetty-start/src/test/resources/usecases/alternate.5.assert.txt
new file mode 100644
index 00000000000..312011d73ca
--- /dev/null
+++ b/jetty-start/src/test/resources/usecases/alternate.5.assert.txt
@@ -0,0 +1,11 @@
+## The XMLs we expect (order is important)
+XML|${jetty.home}/etc/base.xml
+XML|${jetty.home}/etc/main.xml
+
+# The LIBs we expect (order is irrelevant)
+LIB|${jetty.home}/lib/base.jar
+LIB|${jetty.home}/lib/main.jar
+LIB|${jetty.home}/lib/other.jar
+
+# The Properties we expect (order is irrelevant)
+PROP|main.prop=value0
diff --git a/jetty-start/src/test/resources/usecases/alternate.5.cmdline.txt b/jetty-start/src/test/resources/usecases/alternate.5.cmdline.txt
new file mode 100644
index 00000000000..974f60e896a
--- /dev/null
+++ b/jetty-start/src/test/resources/usecases/alternate.5.cmdline.txt
@@ -0,0 +1 @@
+--module=base