What file(s) do you have the autonomous in/spread across, and what exactly
did you change?
If it comes to it that you can't figure out what it's doing, I reccomend downloading a new default code file, then re-working your autonomous into it... I know, it's a lot of work to do, but maybe(?) it could be a problem with one of your files...
PS: Also, it could possibly be the compiler? Hate to ask a stupid question, but are you sure you're using the MCC18 compiler v2.4? I don't know if that could cause a problem anyway, but what you have there is strange, so it'd be best to try different things and see what works...
EDIT: I read through it again, I didn't see that you got it working in my first read through. I don't know... I suggest using a program (I think textpad does it -
www.textpad.com) to compare each of your files... your custom code to a newly downloaded default... and see what doesn't line up... That'd be my best advice to you as of now. Otherwise, I'm just as confused as you are.