Yes, it does make sense.
With the batteries' grounds disconnected and you using the DVOM to engine ground (glow plugs) and the battery ground, you are completing the ground circuit to the truck. By reinstalling the negative ground cable, you are no longer completing a circuit to ground through the glow plugs. The technical term for what you have experienced is called "voltage drop".
I'll draw a diagram and you tell me whether or not I'm correct in how you have the DVOM hooked up.
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