I had problem with my Ethernet gateway for a long time being unstable (chronicled here -> http://forum.mysensors.org/topic/1779/ethernet-gateway-unreliable-sort-of)... the radio communication with sensors would work fine, but the Ethernet stack would lock up periodically and lose communication to Vera, as well as ping, telnet, etc.
I don't have the exact same setup you do (most specifically, I have a different Ethernet shield), but a couple of changes have really stabilized my gateway. I can still crash it, at will (mostly when trying to include new sensors), but If I leave it the hell along and don't mess with it, it will run for weeks or months without issue.
The link below was a big part of stabilizing it, but may not be relevant to you with a different Ethernet shield, but the other thing that made a big difference for me was making sure I power my radio separate from the Ethernet shield. It seems that both could not be powered through the Arduino and remain stable. I don't know if the Arduino can't source enough current to support both when the radio is transmitting, or what, but someone else suggested powering the radio separately. So, I have a the shield powered (obviously) through the Arduino, but I power the radio separately outside the Arduino. That didn't fix everything, but it got a LOT more stable after that.
Anyway - may or may not help you, but it did me.
--Steve
my network issue that may or may not apply to you.....
http://forum.mysensors.org/topic/536/problems-with-enc28j60-losing-connection-freezing-using-uipethernet-or-ethershield-read-this/41