This is a complete WAG, but I've had a similar issue with the AMG 6.5L TD in my motorhome and the 6.9L NA in my Ford van.
The problem with the 6.5 - after replacing glow plugs (which were from the original engine, so they needed it), controller, and lift pump (which also was bad) - the culprit was ugly battery grounds on the engine.
The Ford's 6.9 had similar symptoms, but the problem with it was the injector return lines' sucking air when the engine stopped.
'94 Barth 28' Breakaway M/H ("StaRV II") diesel pusher: Spartan chassis, aluminum birdcage construction. Peninsular/AMG 6.5L TD (230HP), 18:1, Phazer, non-wastgated turbo, hi-pop injectors, 4L80E (Sun Coast TC & rebuild, M-H Pan), Dana 80 (M-H Cover), Fluidampr, EGT, trans temp, boost gage. Honda EV-4010 gaso genset, furnace, roof air, stove, microwave/convection, 2-dr. 3-way reefer. KVH R5SL Satellite. Cruises 2, sleeps 4, carries 6, and parties 8 (parties 12 - tested).
Stand-ins are an '02 Cadillac Escalade AWD 6.0L and an '06 Toyota Sienna Limited.