The Cooja/MSPSim network simulation framework is widely used for developing and debugging, but also for performance evaluation of WSN projects. We show in this paper that Cooja is not limited only to the simulation of the Contiki OS based systems and networks, but can also be extended to perform simulation experiments of other OS based platforms, especially that with RIOT OS. Moreover, when performing our own simulations with Cooja and MSPSim, we observed timing inconsistencies with identical experimentations made on actual hardware. Such inaccuracies clearly impair the use of the Cooja/MSPSim framework as a performance evaluation tool, at least for time-related performance parameters. We will present in this paper, as our contributions: On the one hand, how to use Cooja with projects not related to Con-tiki OS; On the other hand, the detailed results of our investigations on the inaccuracy problems, as well as the consequences of this issue, and give possible leads to fix or avoid it.