Some programs execute a simulation multiple times each time they are run, using a different random seed each time. In Drone's terms, the target program is still executing a single run; it just happens to be executing an entire case within that run. To use Drone with such a program, simply set the parameter numRuns to 1 in the control file and configure the rest of the experiment as usual. Each case will then consist of a single run of the target program, which will in turn execute the simulation multiple times for those parameter settings.
An example of this kind of program is John Grefenstette's Genesis 5.0 genetic algorithm package (see Section 3.3.3). Note that Genesis also requires an adapter script in order to be used with Drone; however, this has no connection with the fact that it executes the simulation multiple times.