Make sure that LUFAConfig.h is included *after* the common submodules, so that the architecture and other defines are available to the configuration header.

LUFA/Common/Common.h

@@ -68,16 +68,16 @@
 		#include <string.h>
 		#include <stddef.h>
 
-		#if defined(USE_LUFA_CONFIG_HEADER)
-			#include "LUFAConfig.h"
-		#endif
-
 		#include "Architectures.h"
 		#include "BoardTypes.h"
 		#include "ArchitectureSpecific.h"
 		#include "CompilerSpecific.h"
 		#include "Attributes.h"
 
+		#if defined(USE_LUFA_CONFIG_HEADER)
+			#include "LUFAConfig.h"
+		#endif
+
 	/* Enable C linkage for C++ Compilers: */
 		#if defined(__cplusplus)
 			extern "C" {