Are you sure the vacuum is being released from the shut off diaphragm before you try to start it? It sounds as if there is still partial vacuum on the diaphragm in some conditions, hindering the flow of fuel thru the system. That could be why any slight pressure in the crankcase would activate the diaphragm fully.
Can you explain what mechanism you have in place of the ignition switch that releases the vacuum from the diaphragm prior to starting? It sounds to me from your description of the system that you have a valve which sends vacuum to the shut off valve to shut off the motor. You then turn this valve off to stop vacuum going to the shut off valve to start it. But stopping vacuum going to the shut off valve is not the same as bleeding off the vacuum you induced in the system. I think this is where your problem lies and it's why both motors had the same problem.

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1977 300d 70k--sold 08
1985 300TD 185k+
1984 307d 126k--sold 8/03
1985 409d 65k--sold 06
1984 300SD 315k--daughter's car
1979 300SD 122k--sold 2/11
1999 Fuso FG Expedition Camper
1993 GMC Sierra 6.5 TD 4x4
1982 Bluebird Wanderlodge CAT 3208--Sold 2/13