As sais above, it's just the diesel particle filter going through a regeneration cycle. The engine management computer triggers this once every 500 - 600 miles. Often you may not even notice it, as it will take place while you're driving at speed.
Having owned a new Mondeo IV 2.0 TDCI for three and a half years and nearly 40,000 miles (same underpinnings and very similar engine), the DPF system in these cars seems robust -- very few reported DPF problems on Ford S-Max / Mondeo forums.
One comment I would make, the 2.2 high-power diesel is not noted for its good economy. It may be worth considering the 2.0 TDCI with 163bhp as an alternative. It should be a fair bit cheaper too.
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