Just recently, my 06 d4d hilux has been running like crap everytime you start after its been sitting for at least 5 mins. I've noticed that when you shut it off, you can hear fluid from around the pump/rail area running back and gurgling through the system. If left long enough, it actually will stall unless I give it some pedal. After a few seconds of running like shit, it smooths out and you can hear the injectors working properly. It runs beautifully once it's past this stage, no 'injector knocks'. It's done 212,000ks, but has already had I think 3 injectors replaced.
Here is a video of the problem: http://www.youtube.com/watch?v=ipy-q-QJg3Y
Cheers.