Eduardo, I don't think you have to worry about using Onyx for repairing permissions. Just like Cocktail, this program does nothing by itself. It's just a GUI front-end to a bunch of OSX/Unix system utilities, most of which you'd otherwise access through Terminal commands. In fact, that's just what it does - it issues Terminal commands according to the way you've configured it's settings.
I mostly use Onyx in its automated mode to run system routines, clean up caches and repair permission before system upgrades etc. Then, after the update, I use Disk Utility to do the permission repair alone - just because it's faster to do it that way when that's the only thing I want. As far as I know, both programs use the same system routine.
And, Rob, when you're using Sharepoints as a cheap replacement for OSX Server, as I do, you might find it necessary to not only repair, but change permissions on certain folders or on the complete shared volume once in a while. For example, if you use the server machine to create a new folder in the shared volume, you might find you can't write from networked machines to the new folder because it was created with the server admin as the owner and only read access for others.
To fix that situation, use BatchMod:
http://macchampion.com/arbysoft/
Take care not to change Owner of Archicad files - AC won't like that. But you can let all participants Read and Write, which will fix the situation you described. And never use BatchMod on any system files!
AC4.1-AC26SWE; MacOS13.5.1; MP5,1+MBP16,1