I am having the same issue using the PCBSD9.1-RELEASE-04-12-2013-x64-DVD.iso for installation. Default install except I used UFS instead of ZFS.
I did a fresh install with this disc 3 weeks ago and AppCafe worked perfectly. Today I perform another fresh PCBSD install, however this time AppCafe gives me the "Missing meta-files for RepoID: 001" error.
and got a reply that the index files will soon refresh, but it never happens. My /var/db/pbi/index directory is empty.
/var/log/pbid.log shows that pbid started, but no other activity.
Is there any repository I can add to the AppCafe repository list which will enable me to install PBIs? Would you recommend I just go directly to one of the mirrors, grab the PBIs I need and install them directly? Is there a way I can manually grab the index file from somewhere?