Suggest you look for an air leak into the fuel system - perhaps just before the injection pump.
If air is drawn into the fuel system when the engine is shut down, then, upon start up, that air will enter the injection pump and prevent the pump from delivering full opening pressure to the injectors. After the tiny air bubble has been expelled the engine runs normally.
Check the fuel line fittings, filters and clamps etc. in the supply line before the fuel pump and injection pump.