My environment: CUC 22.214.171.12400-26
I've found that the Unity Connection Licensing quite confusing. For a CUC cluster, it will ship with 3 PAKs, 2 of them contains mailboxes, ports and feature license, the HA PAK contains port licenses only.
The first 2 PAKs should be registered with the publisher license mac, and upload from the CUC publisher admin page.
The HA PAK should be registered with the subscriber license mac, and upload from the CUC subscriber admin page.
At the end you should have port licenses evenly distributed across the pub and sub, and mailboxes and features bind to the publisher.
If you found the license file is invalid when you upload to CUC, make sure you are NOT using Mac OS X + Entourage and download the files via Entourage. It will corrupt the file, the workaround I've done is to download the license files via OWA, and it works!
Hope it will make it clear and save some time to deal with the licensing team!