Using Designer 4.5.3 on Windows Server 2012 R2.

I have a package that I want to create a new version for, it contains 1
GCV and 2 PRDs and two resources (GCVs-prompt and upgrade settings).

But when I create a new version only the GCV and resources get copied to
the new package version, not the PRDs which kind of defeats the purpose
of packaging.

Has anybody else had the same issue?