Okay, I've looked at my response from last night again, and I still think you're wrong about the CO2 content of diesel exhaust. Excluding N, CO2 should be the largest fraction of the exhaust, with H2O a close (often ignored) second. CO, HC, and NOx are produced in much smaller quantities than CO2 (a couple of orders of magnitude - 100x smaller).
I'm not sure what your cooling system configuration is, but it's my guess that it's similar to the following:
There is a "closed" (pressurized) system that can only be safely filled when the engine is cold. The radiator cap regulates pressure in this portion of the system
There is an "open" (non-pressurized) recovery (or "expansion"

tank that captures coolant that is vented past the radiator cap.
The problem you're having, if I read it right, is that coolant that goes into the recovery tank is not being sucked back into the radiator?
If I've gotten all that right, my suggestions are:
Check the radiator cap to make sure it's not allowing leaks to atmosphere (you've replaced it, so check that off the list)
Check the hose from the radiator outlet to the expansion tank for leaks
Check that the expansion tank end of the hose is at the BOTTOM of the tank, so that it is completely submerged in coolant.