diff --git a/app/src/processing/app/debug/AvrdudeUploader.java b/app/src/processing/app/debug/AvrdudeUploader.java
index 7afec04b4..dbfdd9b88 100755
--- a/app/src/processing/app/debug/AvrdudeUploader.java
+++ b/app/src/processing/app/debug/AvrdudeUploader.java
@@ -30,6 +30,7 @@ import processing.app.Base;
 import processing.app.Preferences;
 import processing.app.Serial;
 import processing.app.SerialException;
+import static processing.app.I18n._;
 
 import java.io.*;
 import java.util.*;
@@ -63,36 +64,53 @@ public class AvrdudeUploader extends Uploader  {
       return avrdude(params);
     }
 
-    return uploadViaBootloader(buildPath, className);
+    return uploadViaBootloader(buildPath, className);  
+  }
+  
+  private static String selectLeonardoUploadPort() {
+  	String names[] = Serial.list();
+	String result = (String)JOptionPane.showInputDialog(null, processing.app.I18n.format(_("Please select the Leonardo upload port:")), "Select upload port", JOptionPane.PLAIN_MESSAGE, null, names, 0);
+	return result;	
   }
   
   private boolean uploadViaBootloader(String buildPath, String className)
-  throws RunnerException, SerialException {
+  		throws RunnerException, SerialException {
     Map<String, String> boardPreferences = Base.getBoardPreferences();
     List commandDownloader = new ArrayList();
     String protocol = boardPreferences.get("upload.protocol");
     
     // avrdude wants "stk500v1" to distinguish it from stk500v2
     if (protocol.equals("stk500"))
-      protocol = "stk500v1";
-      
+      protocol = "stk500v1";      
+    
 	// need to do a little dance for Leonardo and derivatives:
 	// open then close the port at the magic baudrate (usually 1200 bps) first to signal to the 
 	// sketch that it should reset into bootloader.  after doing this wait a moment for the 
-	// bootloader to enumerate
+	// bootloader to enumerate.  On Windows, also must deal with the fact that the COM port number
+	// changes from bootloader to sketch.
+	String leonardoUploadPort = null;
 	if (boardPreferences.get("bootloader.path").equals("caterina_LUFA")) {
     	try {
-    		Serial serial = new Serial(Integer.parseInt(boardPreferences.get("upload.speed")));
-    		serial.dispose();
-		    serial = null;
-		    Thread.sleep(8000);
+    		Serial.touchPort(Preferences.get("serial.port"), 1200);
+    		Thread.sleep(8000);
     	} catch (SerialException ex) { 
-    	} catch (InterruptedException ex) { }    	
+    	} catch (InterruptedException ex) { }
+
+		if (Base.isWindows()) {
+			leonardoUploadPort = selectLeonardoUploadPort();
+			if (null == leonardoUploadPort) 
+				return false;
+		}
     }
     
     commandDownloader.add("-c" + protocol);
-    commandDownloader.add(
-      "-P" + (Base.isWindows() ? "\\\\.\\" : "") + Preferences.get("serial.port"));
+    if (null == leonardoUploadPort) {
+	    commandDownloader.add(
+    	  "-P" + (Base.isWindows() ? "\\\\.\\" : "") + Preferences.get("serial.port"));
+    } else {
+	    commandDownloader.add(
+    	  "-P" + (Base.isWindows() ? "\\\\.\\" : "") + leonardoUploadPort);    
+    }
     commandDownloader.add(
       "-b" + Integer.parseInt(boardPreferences.get("upload.speed")));
     commandDownloader.add("-D"); // don't erase
diff --git a/hardware/arduino/boards.txt b/hardware/arduino/boards.txt
index 89035e690..7d25ab82b 100644
--- a/hardware/arduino/boards.txt
+++ b/hardware/arduino/boards.txt
@@ -149,7 +149,8 @@ mega.build.variant=mega
 leonardo.name=Arduino Leonardo
 leonardo.upload.protocol=avr109
 leonardo.upload.maximum_size=28672
-leonardo.upload.speed=1200
+leonardo.upload.speed=57600
+leonardo.upload.disable_flushing=true
 leonardo.bootloader.low_fuses=0xde
 leonardo.bootloader.high_fuses=0xd8
 leonardo.bootloader.extended_fuses=0xcb
diff --git a/hardware/arduino/cores/arduino/CDC.cpp b/hardware/arduino/cores/arduino/CDC.cpp
index 6dd1cbee9..deda5c08b 100644
--- a/hardware/arduino/cores/arduino/CDC.cpp
+++ b/hardware/arduino/cores/arduino/CDC.cpp
@@ -23,20 +23,6 @@
 #if defined(USBCON)
 #ifdef CDC_ENABLED
 
-void Reboot()
-{
-	USB.detach();
-	cli();
-
-	// Reset the microcontroller to run the bootloader
-	wdt_enable(WDTO_15MS);
-	for (;;);
-}
-
-// Define constants and variables for buffering incoming serial data.  We're
-// using a ring buffer (I think), in which head is the index of the location
-// to which to write the next incoming character and tail is the index of the
-// location from which to read.
 #if (RAMEND < 1000)
 #define SERIAL_BUFFER_SIZE 16
 #else
@@ -114,9 +100,14 @@ bool WEAK CDC_Setup(Setup& setup)
 
 		if (CDC_SET_CONTROL_LINE_STATE == r)
 		{
-			if (0 != _usbLineInfo.lineState && 1200 == _usbLineInfo.dwDTERate)	// auto-reset is triggered when the port, already open at 1200 bps, is closed
-				Reboot();
 			_usbLineInfo.lineState = setup.wValueL;
+			// auto-reset into the bootloader is triggered when the port, already 
+			// open at 1200 bps, is closed.  this is the signal to start the watchdog
+			// with a relatively long period so it can finish housekeeping tasks
+			// like servicing endpoints before the sketch ends
+			if (0 != _usbLineInfo.lineState && 1200 == _usbLineInfo.dwDTERate) {	
+				wdt_enable(WDTO_2S);
+			}
 			return true;
 		}
 	}