The result of a Capacitance Analysis is a capacitance matrix.
A capacitance matrix consists of multiple columns. Each column represents an "active" conductor and there you will find its self capacitance and the mutual capacitance to all other conductive parts.
This means that every time you select a second active part, you ask SENSE to simulate a second capacitance column.
The more active parts selected, the more the simulation will last. The time increases linearly, 2 parts will take twice as much time.