Kind of interesting how this has only seemingly affected me and none of the other many users of the RFM69 :/

Thanks for the help and pointing me in the right direction scalz!

void preHwInit(void)
{
  // Reset the RFM69 Radio
  pinMode(5, OUTPUT);
  digitalWrite(5, HIGH);
  delayMicroseconds(100);
  digitalWrite(5, LOW);
  // wait until chip ready
  delay(5);
}

MyTransportRFM69.cpp

bool transportInit(void)
{
+    // Reset the RFM69 Radio
+    pinMode(5, OUTPUT);
+    digitalWrite(5, HIGH);
+    delay(100);
+    digitalWrite(5, LOW);
+    delay(100);

    // Start up the radio library (_address will be set later by the MySensors library)
    if (_radio.initialize(MY_RFM69_FREQUENCY, _address, MY_RFM69_NETWORKID)) {
#ifdef MY_RFM69_ENABLE_ENCRYPTION

Once those lines to reset it were added it works flawlessly every time now :confused:
The adafruit breakout has a pull-high on the RST pin and as far as I'm aware reading the RFM69 datasheet, it does a power on reset also, so I'm not sure why this is neccessary.

The Hardware I'm using is an Arduino Pro mini (3.3v) and an RFM69HCW on the Adafruit breakout board.

The LPL sketch that works is below, as for the MySensors one It's basically just the examples (as a serial gateway and node) that won't work.

// Sample RFM69 sender/node sketch, with ACK and optional encryption, and Automatic Transmission Control
// Sends periodic messages of increasing length to gateway (id=1)
// It also looks for an onboard FLASH chip, if present
// **********************************************************************************
// Copyright Felix Rusu 2016, http://www.LowPowerLab.com/contact
// **********************************************************************************
// License
// **********************************************************************************
// This program is free software; you can redistribute it
// and/or modify it under the terms of the GNU General
// Public License as published by the Free Software
// Foundation; either version 3 of the License, or
// (at your option) any later version.
//
// This program is distributed in the hope that it will
// be useful, but WITHOUT ANY WARRANTY; without even the
// implied warranty of MERCHANTABILITY or FITNESS FOR A
// PARTICULAR PURPOSE. See the GNU General Public
// License for more details.
//
// Licence can be viewed at
// http://www.gnu.org/licenses/gpl-3.0.txt
//
// Please maintain this license information along with authorship
// and copyright notices in any redistribution of this code
// **********************************************************************************
#include <RFM69.h>         //get it here: https://www.github.com/lowpowerlab/rfm69
#include <RFM69_ATC.h>     //get it here: https://www.github.com/lowpowerlab/rfm69
//#include <SPIFlash.h>      //get it here: https://www.github.com/lowpowerlab/spiflash
#include <SPI.h>           //included with Arduino IDE install (www.arduino.cc)

//*********************************************************************************************
//************ IMPORTANT SETTINGS - YOU MUST CHANGE/CONFIGURE TO FIT YOUR HARDWARE ************
//*********************************************************************************************
#define NODEID        2    //must be unique for each node on same network (range up to 254, 255 is used for broadcast)
#define NETWORKID     100  //the same on all nodes that talk to each other (range up to 255)
#define GATEWAYID     1
//Match frequency to the hardware version of the radio on your Moteino (uncomment one):
#define FREQUENCY   RF69_433MHZ
//#define FREQUENCY   RF69_868MHZ
//#define FREQUENCY     RF69_915MHZ
#define ENCRYPTKEY    "sampleEncryptKey" //exactly the same 16 characters/bytes on all nodes!
#define IS_RFM69HW    //uncomment only for RFM69HW! Leave out if you have RFM69W!
//*********************************************************************************************
//Auto Transmission Control - dials down transmit power to save battery
//Usually you do not need to always transmit at max output power
//By reducing TX power even a little you save a significant amount of battery power
//This setting enables this gateway to work with remote nodes that have ATC enabled to
//dial their power down to only the required level (ATC_RSSI)
//#define ENABLE_ATC    //comment out this line to disable AUTO TRANSMISSION CONTROL
// #define ATC_RSSI      -80
//*********************************************************************************************

#ifdef __AVR_ATmega1284P__
  #define LED           15 // Moteino MEGAs have LEDs on D15
  #define FLASH_SS      23 // and FLASH SS on D23
#else
  #define LED           9 // Moteinos have LEDs on D9
  #define FLASH_SS      8 // and FLASH SS on D8
#endif

#define SERIAL_BAUD   38400

int TRANSMITPERIOD = 200; //transmit a packet to gateway so often (in ms)
char payload[] = "123 ABCDEFGHIJKLMNOPQRSTUVWXYZ";
char buff[20];
byte sendSize=0;
boolean requestACK = false;
// SPIFlash flash(FLASH_SS, 0xEF30); //EF30 for 4mbit  Windbond chip (W25X40CL)

#ifdef ENABLE_ATC
  RFM69_ATC radio;
#else
  RFM69 radio;
#endif

void setup() {

  pinMode(5, OUTPUT);
  digitalWrite(5, HIGH);
  delay(100);
  digitalWrite(5, LOW);
  delay(100);

  Serial.begin(SERIAL_BAUD);
  radio.initialize(FREQUENCY,NODEID,NETWORKID);
#ifdef IS_RFM69HW
  radio.setHighPower(); //uncomment only for RFM69HW!
#endif
  radio.encrypt(ENCRYPTKEY);
  //radio.setFrequency(919000000); //set frequency to some custom frequency

//Auto Transmission Control - dials down transmit power to save battery (-100 is the noise floor, -90 is still pretty good)
//For indoor nodes that are pretty static and at pretty stable temperatures (like a MotionMote) -90dBm is quite safe
//For more variable nodes that can expect to move or experience larger temp drifts a lower margin like -70 to -80 would probably be better
//Always test your ATC mote in the edge cases in your own environment to ensure ATC will perform as you expect
#ifdef ENABLE_ATC
  radio.enableAutoPower(ATC_RSSI);
#endif

  char buff[50];
  sprintf(buff, "\nTransmitting at %d Mhz...", FREQUENCY==RF69_433MHZ ? 433 : FREQUENCY==RF69_868MHZ ? 868 : 915);
  Serial.println(buff);

#ifdef ENABLE_ATC
  Serial.println("RFM69_ATC Enabled (Auto Transmission Control)\n");
#endif
}

long lastPeriod = 0;
void loop() {
  //process any serial input
  if (Serial.available() > 0)
  {
    char input = Serial.read();
    if (input >= 48 && input <= 57) //[0,9]
    {
      TRANSMITPERIOD = 100 * (input-48);
      if (TRANSMITPERIOD == 0) TRANSMITPERIOD = 1000;
      Serial.print("\nChanging delay to ");
      Serial.print(TRANSMITPERIOD);
      Serial.println("ms\n");
    }

    if (input == 'r') //d=dump register values
      radio.readAllRegs();
    //if (input == 'E') //E=enable encryption
    //  radio.encrypt(KEY);
    //if (input == 'e') //e=disable encryption
    //  radio.encrypt(null);
  }

  //check for any received packets
  if (radio.receiveDone())
  {
    Serial.print('[');Serial.print(radio.SENDERID, DEC);Serial.print("] ");
    for (byte i = 0; i < radio.DATALEN; i++)
      Serial.print((char)radio.DATA[i]);
    Serial.print("   [RX_RSSI:");Serial.print(radio.RSSI);Serial.print("]");

    if (radio.ACKRequested())
    {
      radio.sendACK();
      Serial.print(" - ACK sent");
    }
    Serial.println();
  }

  int currPeriod = millis()/TRANSMITPERIOD;
  if (currPeriod != lastPeriod)
  {
    lastPeriod=currPeriod;

  Serial.print("Sending[");
  Serial.print(sendSize);
  Serial.print("]: ");
  for(byte i = 0; i < sendSize; i++)
  Serial.print((char)payload[i]);

  if (radio.sendWithRetry(GATEWAYID, payload, sendSize))
  Serial.print(" ok!");
  else Serial.print(" nothing...");


    sendSize = (sendSize + 1) % 31;
    Serial.println();
  }
}

looks strange.
Actually you don't need to reset the rfm69 with Mysensors nor Lowpowerlab libs. But that will be an upcoming, optional feature in the next driver.

What's your hardware and sketch?