I teach middle school STEM through Project Lead the Way. I have about 30 VEX Cortexes that I am having the same issue with.

I cannot get any Cortex to run any program after disconnecting the Cortex from the computer unless I turn the Cortex off and back on in bootload mode. I have updated the Master CPU firmware and the firmware on every Cortex we have. The Cortex (all of them) ROBOT light and VEXnet lights flash amber. At present moment, I can't recall what the GAME light does. I'll check and post when I return to my school.

The programs all run fine when the Cortex is connected to the computer and we run the debug. The programs also run fine when we reset the Cortex in bootload mode but they only run once, then the students must put the Cortex in bootload mode again if they want to run their robots again.

I would suggest first taking a look through the 'Getting Started with a VEX Cortex' ROBOTC wiki guide, as it walks through all of the steps and settings to use a Cortex with ROBOTC; there may be one or two steps you are missing that are causing this problem.

When you say you turn the Cortex back on in 'bootload' mode, what do you mean exactly by that? When you turn the Cortex's back on, is the Config button on the Cortex being pressed or are the robots simply being turned on? To start a program with a Cortex that is not connected to the computer, all you should have to do is power cycle the Cortex; it will then start the program from the start of task main().