However when proceeding to the last step in the guide and creating the renew script I run into trouble. Rather than renewing my certificate it just seem to generate new certificates and import these into server.app.
You are aware there is no such thing as renewals in SSL Certificates. It's called a renewal for understanding but once a cetificate is issued it cannot be altered in any way (including adding a new valid date range).
So in fact what the script is doing is correct i.e. issuing a new certificate that is valid for 90 days.
Have a read of this chain which describes the behavior. Although it talks about expand the renewal concept is the same.
Andrei