I got the problem resolved right after qualification matches today (I know, it's late) and the problem was it was hanging in a while loop, and it didn't want to kick out. With the help of Matt from team 2619, we added a tick count, and used that to kill the while loops. Now, if executed just right, autonomous will not give the user control for (up to) the first 8-ish seconds, but the team is OK with that for right now. Too bad chain keeps popping off and our wheel brackets are bending...
