For it driving in reverse:
Do you have the motor invert booleans setup right for your wiring in begin.vi?
If this was the case, you should see similar issues in teleop, but it sounds like you are creating seperate dev. Ref.s for auto and teleop. you shouldn't be doing that - I'm not sure if opening two drives pointing to the same pwm channels will break something, but you certainly shouldn't need to do it this way. If you want to do it that way, I would at least try to close the drive when auto finishes, and then open the drive w/ holonomic after.
I would suggest watching this video @ frc master, it should help resolve any lingering questions you have about how the default code is supposed to work
http://www.frcmastery.com/labview-fo...tonomous-code/