Issues in hierarchy in Portfolio for JIRA are not linked automatically

We are using a SAFe-like setup in JIRA with the issues types:

Portfolio Epics -> Capability -> Feature or Epic -> Story

For issues of each issue type we use different JIRA projects. In Portfolio we have configured the Hierarchy in the same way:

Portfolio Epics -> Capability -> Feature or Epic -> Story

After configuring the JIRA projects to use in Portfolio I can see all issues, but they are not shown in a hierarchy (except issues with Epic/Story Link in same project). I configured the Parent Link manually for a couple of issues, and then the hierarchy is shown correctly. But doing this for all our issues manually would be a huge maintenance pain (we have a lot of issues). 

Am I missing something here? I was expecting that the hierarchy is constructed and maintained automatically based on the Portfolio Hierarchy Config. Any help is appreciated.

We are using JIRA Server 7.4.2 and Portfolio 2.5.

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