Thanks for the serial number.

 I looked up how that engine left the factory and it DOES NOT have a CAT hand priming pump on it.

So, I recommend you get one and its gasket.



Here's what I feel is happening with engine. When it is running, it has roughly 70-90 psi of fuel pressure in the CAT fuel line, fuel filter base, secondary fuel filter, fuel rail manifold, passages in the cylinder head and around the injectors. 

Now, WITHOUT a CAT hand pump, you shutoff the engine, IF your return line check valve is still in good working condition, all that pressure and volume of fuel is no longer getting "pumped" TOWARDS the engine, it is looking for a way out(path of least resistance) In this case: going backwards, thru the fuel transfer pump and thru the truck's primary fuel filter(on the framerail) and back to the tank.
 
Now, why is this "not-so-good"?   Because,  the primary fuel filter usually has some air trapped in it, and when fuel pushed backwards, it tends to aerate the truck's fuel lines to the fuel tanks and they lose their prime.
Now, when you crank the engine, the next time; It is "hit or miss" whether the engine's fuel transfer pump can get primed again, to provide fuel volume and pressure to the CAT engine's injectors so they can squirt in fuel while cranking.  This "hit or miss" senario, is why it can be intermittent problem.

By ADDING a CAT fuel hand pump, you have added some one-way check valves into the fuel system, thus the fuel pressure/volume can no longer travel backwards = a good thing. It is trapped in the secondary fuel filter, the fuel filter base, the fuel rail, the cylinder head; then over time it slowly leaks/seeps by the fuel return check valve and goes back to the tank THRU THE RETURN LINE from the engine(not the supply line/hose)

There is also a possibility that your truck maybe "sucking air" ,a little, and thus this type of problem is multiplied, because more "air" is in the truck's fuel supply system already and probably more "air" in the primary fuel filter, too.