Thanks the best lead I have at the moment is from a Peugeot forum (same engine). This is the quote :
"Hi everyone, I am an experienced independant mechanic. I work alot at HDI's. Basically what is happening is that your car is requesting regeneration assistance every say 400 mile or 600 KM, ie you will only experience the problem at these intervals. It will start the regen say 10 - 15 mins after starting car. During regen the car bypasses the intercooler. It does this by closing the top doser valve and opening the bottom valve. Your cars are closing the top valve but not opening the bottom. This chokes the car of air and to prevent stalling opens and closes the top doser. The car will rev up and down from 500 to 1500 rpm on idle and give out bursts of smoke from exhaust. it will also lack power and chug alot until it hits higher revs. The 3 things that can cause this is the bottom doser is broken (ie flaps about loose when hose is removed), the second is a vacuum problem ie leak from pipe etc and the third is a faulty solenoid which is at the bottom left on front of engine, 2 bolted togeather and they are both brown, i think the bottom doser is the back solenoid next block, i cant remember. If you pull vacuum pipe off top doser when the car is idling erratically it should let it idle smooth. It may not be safe to drive with it disconnected incase the dosers close for engine braking? Im not sure. "