PDI NVM enable is fast enough that bare polling is enough without a fixed delay in between each attempt. Make sure the USART transmitter is enabled explicitly when the USART is configured, so that repeated attempts to re-enter PDI mode don't fail due to TXEN not being set.

Projects/AVRISP/Lib/PDIProtocol.c

@@ -115,11 +115,9 @@ static void PDIProtocol_EnterXPROGMode(void)
 	  PDITarget_SendByte(PDI_NVMENABLE_KEY[i - 1]);
 
 	/* Poll the STATUS register to check to see if NVM access has been enabled */
-	uint8_t NVMAttemptsRemaining = 150;
+	uint8_t NVMAttemptsRemaining = 255;
 	while (NVMAttemptsRemaining)
 	{
-		_delay_ms(1);
-
 		PDITarget_SendByte(PDI_CMD_LDCS | PD_STATUS_REG);
 		if (PDITarget_ReceiveByte() & PDI_STATUS_NVM)
 		  break;

Projects/AVRISP/Lib/PDITarget.c

@@ -173,6 +173,7 @@ void PDITarget_EnableTargetPDI(void)
 	/* Set up the synchronous USART for XMEGA communications - 
 	   8 data bits, even parity, 2 stop bits */
 	UBRR1  = 10;
+	UCSR1B = (1 << TXEN1);
 	UCSR1C = (1 << UMSEL10) | (1 << UPM11) | (1 << USBS1) | (1 << UCSZ11) | (1 << UCSZ10) | (1 << UCPOL1);
 
 	/* Send two BREAKs of 12 bits each to enable PDI interface (need at least 16 idle bits) */
@@ -182,9 +183,10 @@ void PDITarget_EnableTargetPDI(void)
 
 void PDITarget_DisableTargetPDI(void)
 {
-	/* Turn of receiver and transmitter of the USART, clear settings */
-	UCSR1B = 0;
-	UCSR1C = 0;
+	/* Turn off receiver and transmitter of the USART, clear settings */
+	UCSR1A |= (1 << TXC1) | (1 << RXC1);
+	UCSR1B  = 0;
+	UCSR1C  = 0;
 
 	/* Set all USART lines as input, tristate */
 	DDRD  &= ~((1 << 5) | (1 << 3));