Research of potential socio-economic value is often conducted within cross-sector (government, university, business) centres. There has been growing interest among science policy researchers in seeking to understand the organizational dilemmas confronted in cross-sector research collaboration. While there is clearly a coalition of interests among partners engaged with collaborative research their broader organizational objectives and strategies may converge, diverge, or even compete. Yet little empirical evidence exists on (a) how individual researchers perceive the benefits of their participation, (b) how far the structures and functions of particular collaborative R&D centres coalesce around of researchers’ expectations and, (c) what problems arise for researchers who opt for a ‘second job’ in the centre. Within the broad policy and organizational context of the Australian Cooperative Research Centres this chapter presents a qualitative analysis of a survey of respondents from public sector organizations and universities involved in the centres. We use the perspective of the individual research scientists to illuminate the management issues of trust, governance, and competition between functional domains, which emerge from the field of inter-organizational relationships (IOR) and which have been inadequately recognized in the context of collaborative R&D centres. The findings have implications for the management of the centres, for the careers of research scientists and for public policy.