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My 2006 Honda Civic VTI-L automatic has done 158,000km to date. When I first start the vehicle in the morning, then select reverse gear while my foot is on the brake, there is a shudder which lasts for about 45 seconds. During that time if I select neutral or drive there is no shudder and the problem does not happen for the rest of the day. The vehicle had an automatic gearbox service at 120,000km with a Honda dealer.
Those symptoms definitely point to something amiss in the auto, so head to a transmission specialist. You'll get expert service and it's also likely to be cheaper than at a Honda dealer.