I saw this bug tonight on last year's controller. I am not using any fixes yet, because I didn't think that this was such a huge issue.
Mine went into autonomous mode. All by itself. Even though the competition jumper was connected and set to disable. This is a *serious safety issue*. More than one light was amber on the RC; I think it was the bottom two. I can't remember for sure because I saw it, went "what the..?" and hit reset a few times. For about 2 minutes the controller was strange, not obeying joystick commands, shifting (or trying to, there was no air in the pneumatics), and running auton intermittently (YEA! Another intermittent error!

). I re-programmed the controller more than once, with slightly different codes (I added a printf to see if it really was auton running; I couldn't believe it).
I will try the linker script. I already had new libraries compiled in, so those aren't the cure. I hate that I have to use a "beta-ish" fix, but if that's all there is, that's what I'll use. This is the first time in the whole year and a half we've had that controller that I've seen that error. May it never come back!
Hopefully IFI gets it straightened out quick!
JBot