Well, how about starting by figuring out what is changing between versions of the config file. You haven't given us anything to go on, but here are some possibilities:
- Maybe you are writing a timestamp into the file. Naturally, that will change every time you apply the catalog, even if the meaning of the config file is unaffected by the change.
- Maybe you are writing the same configuration details in different orders.
- Maybe you are adding comments or blank lines.
- Maybe you are adding duplicate entries.
- Or maybe the semantic content of the file is actually changing -- for instance, you could be flip-flopping between two variations on the file.
All of those are things I've seen or heard about in other contexts, but it may also be that you've discovered something new.
Once you know what's changing, you should have a better idea what to look for in your manifests, and where to find it.
John