Hi Simon,
I had the same problem one year ago.
I was testing a Xtreme ECU with the Viper V10 8.3 2003, with the 5.6.4.3240 firmware version (the lastest available in the moment), and had the same problem, 2 cylinders turned off (went to 0 in the firing order) when cranking inmediately went to 0. Never found a solution.
With the new firmware, is 100% sure that the problem disapear? I would like to install again the ECU but I have to confirm that will work.
Thanks