I have constructed a query which returns all site collections and webs. This query is then transformed into a tree and used to display a list of all sites a user have access to.
The query was not returning all items from the index. If I searched for the sites manually the sites was returned.
When setting "TrimDuplicates" to false all items are returned, but one can also set "TrimDuplicatesOnProperty" to "Path" instead. It have the same effect as setting TrimDuplicates to false.