The difference in voltage between the 2 input modes should not occur if everything is correctly connected. When an input floats up to the maximum level, this often indicates there is an open circuit.
To check your setup, I suggest you initially try using a MAX test panel to measure channels under differential mode.You need to refer to the manual of the 2090 on how to connect up for using differential mode. The setup requires switches S1 to S8 be set to diff mode and then a connection made to only the first 8 BNC connectors.The inner and outer parts of the BNC, form the 2 input connections to the DAQ card.
SimonS