Rank-based inference methods are applied in various disciplines, typically when procedures relying on standard normal theory are not justifiable, for example when data are not symmetrically distributed, contain outliers, or responses are even measured on ordinal scales. Various specific rank-based methods have been developed for two and more samples, and also for general factorial designs (e.g., Kruskal-Wallis test, Jonckheere-Terpstra test). It is the aim of the present paper (1) to demonstrate that traditional rank-procedures for several samples or general factorial designs may lead to paradoxical results in case of unbalanced samples, (2) to explain why this is the case, and (3) to provide a way to overcome these disadvantages of traditional rankbased inference. Theoretical investigations show that the paradoxical results can be explained by carefully considering the non-centralities of the test statistics which may be non-zero for the traditional tests in unbalanced designs. These non-centralities may even become arbitrarily large for increasing sample sizes in the unbalanced case. A simple solution is the use of socalled pseudo-ranks instead of ranks. As a special case, we illustrate the effects in sub-group analyses which are often used when dealing with rare diseases.