Make sure the peripheral driver .c files include the driver dispatch header, rather than the architecture specific header files.

LUFA/Drivers/Peripheral/AVR8/Serial_AVR8.c

@@ -29,7 +29,7 @@
 */
 
 #define  __INCLUDE_FROM_SERIAL_C
-#include "Serial.h"
+#include "../Serial.h"
 
 FILE USARTSerialStream;
 

LUFA/Drivers/Peripheral/AVR8/TWI_AVR8.c

@@ -6,7 +6,7 @@
 */
 
 #define  __INCLUDE_FROM_TWI_C
-#include "TWI.h"
+#include "../TWI.h"
 
 uint8_t TWI_StartTransmission(const uint8_t SlaveAddress,
                               const uint8_t TimeoutMS)

LUFA/Drivers/USB/Core/UC3B/Endpoint_UC3B.h

@@ -29,7 +29,7 @@
 */
 
 /** \file
- *  \brief USB Endpoint definitions for the UC3B microcontrollers.
+ *  \brief USB Endpoint definitions for the AVR32 UC3B microcontrollers.
  *  \copydetails Group_EndpointManagement_UC3B
  *
  *  \note This file should not be included directly. It is automatically included as needed by the USB driver

LUFA/Drivers/USB/Core/UC3B/OTG_UC3B.h

@@ -29,7 +29,7 @@
 */
 
 /** \file
- *  \brief USB OTG definitions for the UC3B microcontrollers.
+ *  \brief USB OTG definitions for the AVR32 UC3B microcontrollers.
  *  \copydetails Group_OTG_UC3B
  *
  *  \note This file should not be included directly. It is automatically included as needed by the USB driver
@@ -38,7 +38,7 @@
 
 /** \ingroup Group_OTG
  *  \defgroup Group_OTG_UC3B USB On The Go (OTG) Management (UC3B)
- *  \brief USB OTG definitions for the UC3B microcontrollers.
+ *  \brief USB OTG definitions for the AVR32 UC3B microcontrollers.
  *
  *  Architecture specific USB OTG definitions for the Atmel 32-bit AVR UC3B microcontrollers.
  *

LUFA/Drivers/USB/Core/UC3B/Pipe_UC3B.h

@@ -29,7 +29,7 @@
 */
 
 /** \file
- *  \brief USB Pipe definitions for the UC3B microcontrollers.
+ *  \brief USB Pipe definitions for the AVR32 UC3B microcontrollers.
  *  \copydetails Group_PipeManagement_UC3B
  *
  *  \note This file should not be included directly. It is automatically included as needed by the USB driver