Hi Jonathan
I can't see an easy way around this using the report builder. As I understand it if a user is in more than one organisation the organisations are combined so any organisation they are a member of can be selected.
I think that the organisation values would need to be exported to a spreadsheet or other tool and deaggregated so there is one record for each users's organisation.
Alternatively filtering per organisation and aggregating in the report builder could work but take a long time.
Regards