Philip,
Ultimately all of the Ground channels are connected to the ground of the DAQ board that you are reading the SCXI modules with. What that means for your situation is that if you have one ground at 0 V and another at 28 V, then when you switch to the next module with 28V as the ground then you will likely hurt the DAQ board.
I would recommend sticking to a ground of 0V and then inverting the logic programmatically if that's what is necessary.