diff --git a/dspace-api/src/main/java/org/dspace/core/ConfigurationManager.java b/dspace-api/src/main/java/org/dspace/core/ConfigurationManager.java
index 493b926950..84fb8b8240 100644
--- a/dspace-api/src/main/java/org/dspace/core/ConfigurationManager.java
+++ b/dspace-api/src/main/java/org/dspace/core/ConfigurationManager.java
@@ -507,7 +507,17 @@ public class ConfigurationManager
         
         try
         {
-            String configProperty = System.getProperty("dspace.configuration");
+            String configProperty = null;
+            try
+            {
+                configProperty = System.getProperty("dspace.configuration");
+            }
+            catch (SecurityException se)
+            {
+                // A security manager may stop us from accessing the system properties.
+                // This isn't really a fatal error though, so catch and ignore
+                log.warn("Unable to access system properties, ignoring.", se);
+            }
 
             if (configFile != null)
             {
diff --git a/dspace-jspui/dspace-jspui-api/src/main/java/org/dspace/app/webui/util/FileUploadRequest.java b/dspace-jspui/dspace-jspui-api/src/main/java/org/dspace/app/webui/util/FileUploadRequest.java
index 74db970c5d..1aa6838f66 100755
--- a/dspace-jspui/dspace-jspui-api/src/main/java/org/dspace/app/webui/util/FileUploadRequest.java
+++ b/dspace-jspui/dspace-jspui-api/src/main/java/org/dspace/app/webui/util/FileUploadRequest.java
@@ -55,6 +55,8 @@ import javax.servlet.http.HttpServletRequestWrapper;
 
 import org.apache.commons.fileupload.DiskFileUpload;
 import org.apache.commons.fileupload.FileItem;
+import org.apache.commons.fileupload.servlet.ServletFileUpload;
+import org.apache.commons.fileupload.disk.DiskFileItemFactory;
 import org.dspace.core.ConfigurationManager;
 
 /**
@@ -98,11 +100,15 @@ public class FileUploadRequest extends HttpServletRequestWrapper
         tempDir = ConfigurationManager.getProperty("upload.temp.dir");
         int maxSize = ConfigurationManager.getIntProperty("upload.max");
 
-        DiskFileUpload upload = new DiskFileUpload();
+        // Create a factory for disk-based file items
+        DiskFileItemFactory factory = new DiskFileItemFactory();
+        factory.setRepository(new File(tempDir));
 
+        // Create a new file upload handler
+        ServletFileUpload upload = new ServletFileUpload(factory);
+        
         try
         {
-            upload.setRepositoryPath(tempDir);
             upload.setSizeMax(maxSize);
             items = upload.parseRequest(req);
             for (Iterator i = items.iterator(); i.hasNext();)
diff --git a/dspace-jspui/dspace-jspui-webapp/src/main/webapp/WEB-INF/web.xml b/dspace-jspui/dspace-jspui-webapp/src/main/webapp/WEB-INF/web.xml
index 924b74af52..a1dff39e94 100644
--- a/dspace-jspui/dspace-jspui-webapp/src/main/webapp/WEB-INF/web.xml
+++ b/dspace-jspui/dspace-jspui-webapp/src/main/webapp/WEB-INF/web.xml
@@ -124,6 +124,10 @@
     <url-pattern>/view-workspaceitem</url-pattern>
   </filter-mapping>
 
+    <!-- Listener to clean up Commons-FileUpload -->
+    <listener>
+      <listener-class>org.apache.commons.fileupload.servlet.FileCleanerCleanup</listener-class>
+    </listener>
     <!-- Listener to initialise / clean up the application -->
     <listener>
         <listener-class>org.dspace.app.util.DSpaceContextListener</listener-class>
diff --git a/dspace-lni/dspace-lni-webapp/src/main/webapp/WEB-INF/web.xml b/dspace-lni/dspace-lni-webapp/src/main/webapp/WEB-INF/web.xml
index 23bccf81a9..fcb304339f 100644
--- a/dspace-lni/dspace-lni-webapp/src/main/webapp/WEB-INF/web.xml
+++ b/dspace-lni/dspace-lni-webapp/src/main/webapp/WEB-INF/web.xml
@@ -50,7 +50,12 @@
       The location of the main DSpace configuration file
     </description>
   </context-param>
-  
+
+    <!-- Listener to initialise / clean up the application -->
+    <listener>
+        <listener-class>org.dspace.app.util.DSpaceContextListener</listener-class>
+    </listener>
+    
   <!-- DSpace configuration initialisation.  This needs to be loaded before
        other servlets. -->
   <servlet>
diff --git a/dspace-oai/dspace-oai-webapp/src/main/webapp/WEB-INF/web.xml b/dspace-oai/dspace-oai-webapp/src/main/webapp/WEB-INF/web.xml
index 75d4708b67..a1a7f28029 100644
--- a/dspace-oai/dspace-oai-webapp/src/main/webapp/WEB-INF/web.xml
+++ b/dspace-oai/dspace-oai-webapp/src/main/webapp/WEB-INF/web.xml
@@ -70,6 +70,11 @@
     </description>
   </context-param>
 
+    <!-- Listener to initialise / clean up the application -->
+    <listener>
+        <listener-class>org.dspace.app.util.DSpaceContextListener</listener-class>
+    </listener>
+    
   <!-- DSpace configuration initialisation.  This needs to be loaded before
        other servlets. -->
   <servlet>
diff --git a/dspace-sword/dspace-sword-webapp/src/main/webapp/WEB-INF/web.xml b/dspace-sword/dspace-sword-webapp/src/main/webapp/WEB-INF/web.xml
index 0f2efab4a7..dc80f5aca8 100644
--- a/dspace-sword/dspace-sword-webapp/src/main/webapp/WEB-INF/web.xml
+++ b/dspace-sword/dspace-sword-webapp/src/main/webapp/WEB-INF/web.xml
@@ -39,6 +39,11 @@
   
   <!-- Servlets -->
 
+    <!-- Listener to initialise / clean up the application -->
+    <listener>
+        <listener-class>org.dspace.app.util.DSpaceContextListener</listener-class>
+    </listener>
+    
 <!-- DSpace configuration initialisation.  This needs to be loaded before
        other servlets. -->
   <servlet>
diff --git a/dspace-xmlui/dspace-xmlui-webapp/src/main/webapp/WEB-INF/web.xml b/dspace-xmlui/dspace-xmlui-webapp/src/main/webapp/WEB-INF/web.xml
index db83bea317..c8d39344dc 100644
--- a/dspace-xmlui/dspace-xmlui-webapp/src/main/webapp/WEB-INF/web.xml
+++ b/dspace-xmlui/dspace-xmlui-webapp/src/main/webapp/WEB-INF/web.xml
@@ -49,6 +49,10 @@
         </description>
     </context-param>
 
+    <!-- Listener to clean up Commons-FileUpload -->
+    <listener>
+      <listener-class>org.apache.commons.fileupload.servlet.FileCleanerCleanup</listener-class>
+    </listener>
     <!-- Listener to initialise / clean up the application -->
     <listener>
         <listener-class>org.dspace.app.util.DSpaceContextListener</listener-class>
diff --git a/pom.xml b/pom.xml
index 40187d256e..a17dc3e4f6 100644
--- a/pom.xml
+++ b/pom.xml
@@ -325,12 +325,12 @@
          <dependency>
             <groupId>commons-fileupload</groupId>
             <artifactId>commons-fileupload</artifactId>
-            <version>1.1.1</version>
+            <version>1.2.1</version>
          </dependency>
          <dependency>
             <groupId>commons-io</groupId>
             <artifactId>commons-io</artifactId>
-            <version>1.2</version>
+            <version>1.4</version>
          </dependency>
          <dependency>
             <groupId>commons-lang</groupId>