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Moved to the mk5 specific forum since you have a Jetta.

Correct, it's the active self clean cycle. There is no light or anything to indicate when it's on. During an active self clean while driving, the car burns up the exhaust filter to clean out the trapped particulates. The car also increases turbo boost slightly so you will feel a slightly more powerful engine.

The passive self clean is like a normal catalytic converter which burns up due to the heat from the exhaust. The active cycle activates when the passive doesn't clean it enough.

If you stop the car or if you're at a stoplight, the car runs the fans high to keep the engine compartment cool. Here is some more info on the technical details: http://www.myturbodiesel.com/forum/showthread.php?t=2171 and refer to the buying checklist in the FAQ for some more notes on this. The FAQ articles are constantly revised so these notes may not have been there when you first read it.
 

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Thanks. There are people saying that another software update is coming soon. From what I've read the most recent flash is related to changing the sensitivity of the rear O2 sensor. This guy heard it from the dealer so who knows the accuracy of this statement.

Most modern cars have software updates now. Most of them are done silently when you take the car in for service. They might be for the stereo, car diagnostics, or engine, who knows.

Not sure what that mouse noise is but if you turn the key on/off without starting the engine you can hear the electric motor on the EGR self calibrating. Either that or check for holes in the hood insulation or engine cover from mice.
 
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