Above the Apply button are two buttons to change the quantize mode: Quantize and
Quantize on Track.

The default mode is Quantize, which means that quantization will happen
within selected events. In the case of an Audio Event, this means that transients will be
detected and then quantized. In the case of an Instrument Part, the notes within the part will
be quantized. This mode is equivalent to what happens if you select any Event and press [Q] to
quantize.

If Quantize On Track mode is selected, the selected events themselves will be quantized as
single objects. For instance, if a selected Audio Event starts between two different eighth
notes, and the quantize note value is set to eighth notes, pressing Apply in the Quantize panel
will shift the entire event to start on the nearest eighth note. Note that quantizing with this
mode can only be done by pressing Apply in the Quantize Panel, and using the [Q] keyboard
shortcut will result in the default Quantize mode being used.