I used to understand the system fully but have lost some of that as it's no longer important to me. In short, the CBEA engine line has a complex emissions control system consisting of 3 separate catalytic converters that each must be regenerated from time to time, and two exhaust gas recirculation systems. These regeneration cycles reduce performance and increase fuel consumption.

For example, a DPF regeneration cycle closes a valve in the exhaust which increases system pressure and thus system temperature, while also triggering a post-combustion fuel injection -- injects unburned fuel into the cylinder on the exhaust storke -- to increase the exhaust temperature to burn off soot that accumulates in the particulate filter.

It is likely a change in the schedule of these regeneration events that is necessary to bring the vehicle into compliance.

There is a long PDF[2] that goes into detail how the emissions systems work on these cars.

[1] http://www.myturbodiesel.com/images/dpf3.jpg

[2] http://www.natef.org/natef/media/natefmedia/vw%20files/2-0-t...