The jitter+offset mode for SOFI and ISAAC must be used in case a fundamental assumption cannot be trusted for the normal jitter mode, namely that a pixel sees mostly sky background along time. This is the case for extended objects for example.
Jitter+offset samples the sky background at offsets at least greater than the detector size. Notice that with an 8-m class telescope, there is indeed no empty sky frame, i.e. the photon-collecting power is such that no frame contains truly only sky signal. It is often necessary to filter out spurious astronomical objects from sky frames, by means of a 3d median filter for example. In the case of a jitter+offset observation, the jitter process will perform a median 3d average of all input sky frames (removing effectively spurious astronomical objects), then subtract this sky from all input object frames. The process then goes on as for normal jitter: feature detection, offset estimation, frame registration, and frame stacking.
The software is always working in normal jitter mode, and will switch itself to jitter+offset as soon as at least one frame has been declared as a sky plane in the input list of frames.