Had exactly the same issue in my S Max, a full service (around £200 ) sorted it. Nothing unusual in the ECU, the consensus was it was a clogged fuel filter.
It did get a fuel system flush in the service too though. and oil flush and filter change – doubt it was related but might have helped the turbo out?
Don’t use Tesco fuel. I had the problem for some time, and supermarket fuel made it noticeably worse, Optimax seemed to clear it up a bit (so I filled it with that every so often and stuck to garage forecourts).
I think these new diesels are a bit temperamental.
EDIT: Same 1.8 diesel engine, mines a Titanium which just makes it heavier and makes the problem worse!