The challenges of ensuring equity among partners of very different academic power and status, across continents, within complex research projects involving differing disciplines with their own norms, and balancing needs for capacity development of individuals and for institutions can be major sources of conflicts. While each of these concerns has been addressed separately, the implications of situations where they reinforce each other have not. Drawing on experience in four complex, multi-partner and multi-disciplinary social science research projects, I consider four main overlapping issues: (1) the structural inequalities inherent in North-South relationships as well as between junior and senior researchers and how these raise difficult problems for research managers; (2) the implications of different kinds of local institutions, and of seeing authorship as a major feature of capacity building, even if no funding is allocated to the task within research grants; (3) the effects of multi-disciplinarity: how intellectual property is understood in different disciplinary settings as well as embodied in national or institutional rules, and the implications of these differences in the context of the pressures imposed by institutional review procedures, in particular the Research Excellence Framework in the UK; (4) the challenges to research managers of ensuring that transaction costs do not swamp the possibility of achieving real intellectual additionalities, and how to address the risk that the costs of collaboration outweigh the likely benefits.