Index: src/main/resources/com/zanox/hudson/plugins/FTPPublisher/config.jelly
===================================================================
--- src/main/resources/com/zanox/hudson/plugins/FTPPublisher/config.jelly	(revision 39041)
+++ src/main/resources/com/zanox/hudson/plugins/FTPPublisher/config.jelly	(working copy)
@@ -35,7 +35,7 @@
   </f:entry>
   
   <f:entry title="Flatten files" help="${helpURL}/help-flatten.html">
-    <f:checkbox name="publisher.flatten" checked="${instance.flatten}" />
+    <f:checkbox name="publisher.flatten" checked="${descriptor.isFlatten(instance)}" />
   </f:entry>
   
 </j:jelly>
\ No newline at end of file
Index: src/main/resources/com/zanox/hudson/plugins/FTPPublisher/global.jelly
===================================================================
--- src/main/resources/com/zanox/hudson/plugins/FTPPublisher/global.jelly	(revision 39041)
+++ src/main/resources/com/zanox/hudson/plugins/FTPPublisher/global.jelly	(working copy)
@@ -37,6 +37,9 @@
         </table>
       </f:repeatable>
     </f:entry>
+    <f:entry title="Flatten Files selected by default" help="/plugin/ftppublisher/help-flattenfilesselectedbydefault.html">
+      <f:checkbox name="flattenFilesSelectedByDefault" checked="${descriptor.flattenFilesSelectedByDefault}"/>
+    </f:entry>
   </f:section>
 
 
Index: src/main/webapp/help-flattenfilesselectedbydefault.html
===================================================================
--- src/main/webapp/help-flattenfilesselectedbydefault.html	(revision 0)
+++ src/main/webapp/help-flattenfilesselectedbydefault.html	(revision 0)
@@ -0,0 +1,5 @@
+<div>
+	If this is selected, then the Flatten Files option will be selected by default when a job is first configured to use FTP Publishing.
+	<br/>
+	This option can of course be unselected if a job chooses not to flatten files.
+</div>
Index: src/main/java/com/zanox/hudson/plugins/FTPPublisher.java
===================================================================
--- src/main/java/com/zanox/hudson/plugins/FTPPublisher.java	(revision 39041)
+++ src/main/java/com/zanox/hudson/plugins/FTPPublisher.java	(working copy)
@@ -196,6 +196,9 @@
 
 		private final CopyOnWriteList<FTPSite> sites = new CopyOnWriteList<FTPSite>();
 
+		/** Whether to flatten files by default */
+		private boolean flattenFilesSelectedByDefault;
+
 		/**
 		 * The default constructor.
 		 */
@@ -203,6 +206,15 @@
 			super(FTPPublisher.class);
 			load();
 		}
+		
+		public void setFlattenFilesSelectedByDefault(
+				boolean flattenFilesSelectedByDefault) {
+			this.flattenFilesSelectedByDefault = flattenFilesSelectedByDefault;
+		}
+		
+		public boolean isFlattenFilesSelectedByDefault() {
+			return flattenFilesSelectedByDefault;
+		}
 
 		/**
 		 * The name of the plugin to display them on the project configuration web page.
@@ -258,6 +270,14 @@
 			return pub;
 		}
 
+		public boolean isFlatten(FTPPublisher pub) {
+			if (pub != null) {
+				return pub.isFlatten();
+			} else {
+				return flattenFilesSelectedByDefault;
+			}
+		}
+		
 		/**
 		 * The getter of the sites field.
 		 * 
@@ -284,6 +304,7 @@
 		@Override
 		public boolean configure(StaplerRequest req, JSONObject formData) {
 			sites.replaceBy(req.bindParametersToList(FTPSite.class, "ftp."));
+			flattenFilesSelectedByDefault = formData.getBoolean("flattenFilesSelectedByDefault");
 			save();
 			return true;
 		}