It's been a few weeks since upgrading from 11.1 > 11.2 Monthly update 2. Recently we started seeing odd content errors with some bundles that had previously worked fine, so we ran a novell-zenworks-configure -c CheckContentSystem to see if there was missing content. We had verified our content immediately after the initial upgrade with no reported missing files or db entries. Now after a couple weeks, it is reporting the following.
Server1
Files in Content-Repo, not in DB: 11635 out of 20596
Files in DB, not in Content-Repo: 5906 out of 15376
Server2
Files in Content-Repo, not in DB: 11637 out of 21137
Files in DB, not in Content-Repo: 5906 out of 15376
(Note: we have only uploaded content historically to Server 1 and allow it to replicate to server 2.)

Along with running the CheckContentSystem, we also ran a separate ZDC report which says the following:
Server1: “All 9478 content objects hosted on this server are available”
Server2: “All 10045 content objects hosted on this server are available”
Why the variance in all the numbers and why does zcm now appear to not be cleaning up items from the content-repo or database?
Any help on how to clean up these issues would be helpful.
Thanks!