Single-ended and differential refer to the reference for a voltage. Single-ended is referred to ground while differential is referred to some other voltage. For a single-ended measurement, the LabJack converts the difference between the voltage at an input and ground. For a differential measurement, the LabJack converts the difference between the voltage at one input and the voltage at another input that is not necessarily ground.
Differential does not refer to whether a signal is positive & negative or positive-only. The terms for that are bipolar and unipolar.
On the LabJack U3, U12, U6, and T7, analog inputs can set as single-ended or differential via software. Analog inputs on the LabJack UE9 are single-ended only, so an instrumentation amp is needed to convert a differential signal to single-ended, or a pseudo-differential measurement can be made by taking the difference of two single-ended measurements.
Also see the Differential Readings App Note.