Social cost-benefit analysis is often used to analyse transport investments, and can also be used for transport operation planning and capacity allocation. If it is to be used for resolving capacity conflicts, however, it is important to know whether transit agencies' timetable requests are consistent with the cost-benefit framework, which is based on passenger preferences. We show how a public transport agency's implicit valuations of waiting time and crowding can be estimated by analysing timetables, apply the method to commuter train timetables in Stockholm, and compare the implicit valuations to the corresponding passenger valuations in the official Swedish cost-benefit analysis guidelines. The results suggest that the agency puts a slightly lower value on waiting time and crowding than the passenger valuations codified in the official guidelines. We discuss possible reasons for this and implications for using cost-benefit analysis for capacity allocation. We also find that optimal frequencies are more sensitive to the waiting time valuation than to that of crowding.