This is quite old - but I found this while having the same issues. Solved by moving the NRF24 pins around like this:
// When ENC28J60 is connected we have to move CE/CSN pins for NRF radio
#define MY_RF24_CE_PIN 5
#define MY_RF24_CS_PIN 6
// When ENC28J60 is connected, move SCK, MI and MO pins and enable SPI
#define MY_SOFTSPI
#define MY_SOFT_SPI_SCK_PIN 7
#define MY_SOFT_SPI_MISO_PIN 8
#define MY_SOFT_SPI_MOSI_PIN 9
And of course move the radio pins around.
@BulldogLowell,
I have been having the exact same issues. However, I have finally got inclusion to start working. The trick for me was not down grading the whole IDE, but only downgrading the Boards.
Tools | Board | Board Manager and Searching for AVR. The "Arduino AVT Boards" was at version 1.6.19. which did not work. I downgraded to 1.6.11 and now my GW does not reset and inclusion works.
Give that a try.
PDJ
Re: 
GPS Sensor
Hi,
The example GPS sketch needed a small tweak for it to work with the mysensors integration on Hone Assistant. The semi-colons in the payload message should be comma.
Like this:
sprintf(payload, "%s,%s,%s", latBuf, lngBuf, altBuf);
Cheers.
PDJ
This is quite old - but I found this while having the same issues. Solved by moving the NRF24 pins around like this:
// When ENC28J60 is connected we have to move CE/CSN pins for NRF radio
#define MY_RF24_CE_PIN 5
#define MY_RF24_CS_PIN 6
// When ENC28J60 is connected, move SCK, MI and MO pins and enable SPI
#define MY_SOFTSPI
#define MY_SOFT_SPI_SCK_PIN 7
#define MY_SOFT_SPI_MISO_PIN 8
#define MY_SOFT_SPI_MOSI_PIN 9
And of course move the radio pins around.
I don't think so. The bug sounds like it is with the Ethernet module somehow. A temp/humidity sensor is working ok and it was compiled with the newer version.
@BulldogLowell,
I have been having the exact same issues. However, I have finally got inclusion to start working. The trick for me was not down grading the whole IDE, but only downgrading the Boards.
Tools | Board | Board Manager and Searching for AVR. The "Arduino AVT Boards" was at version 1.6.19. which did not work. I downgraded to 1.6.11 and now my GW does not reset and inclusion works.
Give that a try.
PDJ