I had the same issue with mine. I would run, some times 5 minutes, some times 20 minutes. Then it would shut down and nothing. It would not program with the box. I tried posting on the Viper thread and was told a few things. What I ended up doing was using the Viper software on the PC to program the ecs. I turned off all temp sensing and I have been good to go since.
If you still can not program it, send Viper a message. They have good stuff.
Buzz.