I would be inclined to look for earth currents rather than voltages. Use a scope with a current probe and look out for third harmonics caused by switching power supplies in computers.
I do tend to agree that independent grounds can cause problems.
I'm not quite clear on your diagram as the "isolated ground strip" seems to be connected to the supply ground too (?). Earth loops can be bad news.
Yes, the diagram isn't very clear. The solid green line is connected to the transformer's metal housing. This "bonding" conductor is common to all of the bonding conductors in the room. The green/orange line that comes in through the disconnect switch and carries on over to the transformer along with L1, L2, and bond is an isolated ground that goes all the way back to one of the ground rods in the basement. That same IG terminates at an isolated terminal strip inside the transformer. From the terminal strip a bonding conductor is tied to one side of the secondary creating a neutral. From that same isolated terminal strip another IG carries on to the equipment ground for the TEM.
I really need to go over this whole set-up with the tech because I would like to verify that it is what it should be. Nonetheless, my weekend research found this concerning the transformer:
The most effective tool for control of neutral to ground and common mode disturbances remains the isolation transformer (Figure 4). Isolation transformers allow the bonding of neutral to ground on the transformer secondary. Disturbance current flow now occurs across the impedance of the bonding strap.