diff --git a/Bootloaders/CDC/BootloaderCDC.c b/Bootloaders/CDC/BootloaderCDC.c
index 211b054e3d..7bff89994b 100644
--- a/Bootloaders/CDC/BootloaderCDC.c
+++ b/Bootloaders/CDC/BootloaderCDC.c
@@ -73,7 +73,13 @@ void Application_Jump_Check(void)
 	/* If the reset source was the bootloader and the key is correct, clear it and jump to the application */
 	if ((MCUSR & (1 << WDRF)) && (MagicBootKey == MAGIC_BOOT_KEY))
 	{
+		/* Turn off the watchdog */
+		MCUSR &= ~(1<<WDRF);
+		wdt_disable(); 
+
+		/* Clear the boot key and jump to the user application */
 		MagicBootKey = 0;
+
 		// cppcheck-suppress constStatement
 		((void (*)(void))0x0000)();
 	}
diff --git a/Bootloaders/DFU/BootloaderDFU.c b/Bootloaders/DFU/BootloaderDFU.c
index 233e145ae0..528e8cb0c1 100644
--- a/Bootloaders/DFU/BootloaderDFU.c
+++ b/Bootloaders/DFU/BootloaderDFU.c
@@ -106,11 +106,18 @@ uint32_t MagicBootKey ATTR_NO_INIT;
  */
 void Application_Jump_Check(void)
 {
-	// If the reset source was the bootloader and the key is correct, clear it and jump to the application
+	/* If the reset source was the bootloader and the key is correct, clear it and jump to the application */
 	if ((MCUSR & (1 << WDRF)) && (MagicBootKey == MAGIC_BOOT_KEY))
 	{
+		/* Turn off the watchdog */
+		MCUSR &= ~(1<<WDRF);
+		wdt_disable(); 
+
+		/* Clear the boot key and jump to the user application */
 		MagicBootKey = 0;
-		AppStartPtr();
+
+		// cppcheck-suppress constStatement
+		((void (*)(void))0x0000)();
 	}
 }
 
diff --git a/Projects/AVRISP-MKII/AVRISP-MKII.c b/Projects/AVRISP-MKII/AVRISP-MKII.c
index 71b6da7cd4..c4623fd8e3 100644
--- a/Projects/AVRISP-MKII/AVRISP-MKII.c
+++ b/Projects/AVRISP-MKII/AVRISP-MKII.c
@@ -97,12 +97,12 @@ void EVENT_USB_Device_ConfigurationChanged(void)
 {
 	bool ConfigSuccess = true;
 
-	/* Setup AVRISP Data Endpoint(s) */
+	/* Setup AVRISP Data OUT endpoint */
 	ConfigSuccess &= Endpoint_ConfigureEndpoint(AVRISP_DATA_OUT_EPADDR, EP_TYPE_BULK, AVRISP_DATA_EPSIZE, 1);
 
-	#if defined(LIBUSB_DRIVER_COMPAT)
-	ConfigSuccess &= Endpoint_ConfigureEndpoint(AVRISP_DATA_IN_EPADDR, EP_TYPE_BULK, AVRISP_DATA_EPSIZE, 1);
-	#endif
+	/* Setup AVRISP Data IN endpoint if it is using a physically different endpoint */
+	if ((AVRISP_DATA_IN_EPADDR & ENDPOINT_EPNUM_MASK) != (AVRISP_DATA_OUT_EPADDR & ENDPOINT_EPNUM_MASK))
+	  ConfigSuccess &= Endpoint_ConfigureEndpoint(AVRISP_DATA_IN_EPADDR, EP_TYPE_BULK, AVRISP_DATA_EPSIZE, 1);
 
 	/* Indicate endpoint configuration success or failure */
 	LEDs_SetAllLEDs(ConfigSuccess ? LEDMASK_USB_READY : LEDMASK_USB_ERROR);
diff --git a/Projects/XPLAINBridge/XPLAINBridge.c b/Projects/XPLAINBridge/XPLAINBridge.c
index 3bd1fbf559..7909cc45c5 100644
--- a/Projects/XPLAINBridge/XPLAINBridge.c
+++ b/Projects/XPLAINBridge/XPLAINBridge.c
@@ -226,9 +226,8 @@ void EVENT_USB_Device_ConfigurationChanged(void)
 	{
 		ConfigSuccess &= Endpoint_ConfigureEndpoint(AVRISP_DATA_OUT_EPADDR, EP_TYPE_BULK, AVRISP_DATA_EPSIZE, 1);
 
-		#if defined(LIBUSB_DRIVER_COMPAT)
-		ConfigSuccess &= Endpoint_ConfigureEndpoint(AVRISP_DATA_IN_EPADDR, EP_TYPE_BULK, AVRISP_DATA_EPSIZE, 1);
-		#endif
+		if ((AVRISP_DATA_IN_EPADDR & ENDPOINT_EPNUM_MASK) != (AVRISP_DATA_OUT_EPADDR & ENDPOINT_EPNUM_MASK))
+		  ConfigSuccess &= Endpoint_ConfigureEndpoint(AVRISP_DATA_IN_EPADDR, EP_TYPE_BULK, AVRISP_DATA_EPSIZE, 1);
 
 		/* Configure the V2 protocol packet handler */
 		V2Protocol_Init();