Empirical performance models play an important role in the development of planning portfolios that make a per-domain or per-problem configuration of its search components. Even though such portfolios have shown their power when compared to other systems in current benchmarks, there is no clear evidence that they are capable to differentiate problems (instances) having similar input properties (in terms of objects, goals, etc.) but fairly different runtime for a given planner. In this paper we present a study of empirical performance models that are trained using problems having the same configuration, with the objective of guiding the models to recognize the underlying differences existing among homogeneous problems. In addition we propose a set of new features that boost the prediction capabilities under such scenarios. The results show that the learned models clearly performed over random classifiers, which reinforces the hypothesis that the selection of planners can be done on a per-instance basis when configuring a portfolio.