Solution
The NI 9411 does not need to be configured in software to perform differential or single-ended measurements. The only change will be the connections between the signal or transducer and the module.
In differential mode, the NI 9411 makes a differential measurement between the DIa (positive) and DIb (negative) terminals. The hardware takes the difference between the two inputs and will determine if it's High (between 300 mV and 24 V) or Low (between -300 mV to -24 V).
In single-ended mode, only the positive input terminal is wired for each input and the negative terminal is left floating. The NI 9411 will internally connect the floating negative input line to a reference for single-ended with a High between 2 to 24V and a Low between 0 to 0.8V.
Finally, a user cannot request the software to report the mode the NI 9411 is using. Therefore, it is impossible to detect the connections the device has from a software command.