If you use container.RegisterAutoWiredAs<T,IT>()
then Funq will auto-wire the Repository by convention, i.e. use the largest constructor and resolve and inject each public property dependency of your Repository.
To use an alternate specific constructor, or only autowire specific properties you would have to specify the registration manually with:
container.Register<IOrganisationRepository>(c =>
new OrganisationRepository(c.Resolve<IFoo>()) { Bar = c.Resolve<IBar>() } );
Note: whenever you have IOC issues like this, you should also include the skeleton of your class.