It shouldn't affect the readings at all, if you're seeing that, looking at the schematic of the buffer, I'd suspect that somehow you're getting a 60hz voltage differential between earth ground and the outside track from the transformers. When I do this on my test layout, I see no variation of the DC monitoring voltages regardless of the transformer setting. Even introducing a 100 ohm resistor between earth ground and the buffered output, I don't see a significant change, just about a .2 volt jump. I'm using a TMCC base, and I'm getting 1.25V base and 4.14V boost.
In short, I don't know what's going on. 
With 2-rail, a lot could be different, I have very little experience with TMCC/Legacy on 2-rail of any scale.
