One problem related to automatic transmission control module has been reported for the 2004 Volkswagen Beetle. The most recently reported issues are listed below.
Mechatronic unit failure in transmission. Failure caused car to go into "limp mode" (only able to travel in 1st and 3rd gears, reverse inoperable, car nearly stalled at 20 mph going from 1st to 3rd gear). Repair has been made: $1800 for part, $400 for labor, $200 for rental car during time car was in the shop.