Here's what I've learned following a very painful experience with a new T6 I picked up in December, which they've finally admitted is a dog and are replacing.
When the fan kicks off the van is doing a passive regeneration of the diesel particulate filter, in other words heating it up to burn off the crap. You know it's happening because the rev counter will sit at just under 1000rpm instead of 800rpm and the Stop/Start function will deactivate. After speaking to many people about this the van will perform a passive regen twice during full tank cycle (mine was doing it 4-5 times!) on average. The main downside to these regens apart from that smell is that the ECU sends fuel directly to the DPF to assist with the burning off and your MPG will drop slightly, although mine was falling off the side of a cliff.
Passive regens do not (I'm reliably informed) happen once the tank is below three quarters full, so if you run into the red and keep putting a tenner in it won't regen and you'll get the DPF warning light come on then you have to perform an active regen (driving for 15-20 mins keeping the revs between x and y etc)
As for the smell I noticed that mine was noticeably weaker after about 4000 miles
If however, you go into the red then fill up and the DPF warning light comes on, this may be the early signs of a 'dirty' engine, especially if you're getting nowhere near the MPG you were hoping for. Essentially the engine putting too much crap into the exhaust system and overwhelming it. This is what happened to me, and they've finally given up trying to persuade me that I'm going mental!