So I tested this on my end and didn't see any problems:
1) Install Portal, Server, two web adaptors, and Data Store
2) Create the Portal and Server site
3) Register one web adaptor with Portal and the other web adaptor with Server
4) Register the Data Store with Server
5) Federate Portal and Server and set the Server as the hosting server.
Not sure what was going on initially, but in any case, glad it's sorted for you.