Orange and Red flashing can be caused by trying to run an app with the debug flag turned off. You can replicate it by running Evox, among other thing, on a debug kit. Make sure that any app you run is build with Debug configuration.
And a debug machine can run with a blank EEPROM. Infact, you can rebuild the EEPROM straight from the XDK launcher. Can't help it, but one has got to wonder how a supposedly Problem report turned into an EEPROM request. I'm not even sure if the admins of the board allow such a request.