In this paper, we consider the problem of scheduling a set of jobs on two parallel machines with set-up times. The set-up has to be performed by a single server. The objective is to minimise the forced idle time. The problem of minimising the forced idle time (interference problem) is known to be unary NP-hard for the case of two machines and equal set-up and arbitrary processing times. We propose a mixed integer linear programming model, which describes a special class of schedules where the jobs from a list are scheduled alternatively on the machines, and a heuristic algorithm is tested on instances with up to 100,000 jobs. The computational results indicate that the algorithm has an excellent performance even for very large instances, where mostly an optimal solution is obtained within a very small computational time.