Something is messing with my disk permissions, which breaks a lot of file-related stuff. Can I find out what is causing this? This has been happening for months, and I have no idea what's causing it.

Something on my Mac keeps mucking with disk permissions, and it seems like a trivial set of stuff


Java-related library files and the Applet plugin
Core Graphics headers
Some network headers, like a few files in the arpanet group
My hosts file (in this case, I know that the thing touching the hosts file is the Gasmask application)


However, whatever it is that is doing this, it completely wrenches up a lot of file-related actions.  The two most high-profile issues:


Archive Utility becomes unusable; it hangs indefinitely and I have to force-quit.  3rd party archive utilities like The Unarchiver don't experience this issue, so I've switched to using The Unarchiver.
The most annoying one is that the "Reveal In Finder" action in Alfred doesn't work.  I use this functionality all the time and it constantly stops working.


If there are other issues, I haven't directly noticed them, but I'm sure there are other things I can't find.  Whenever one of these things starts to happen, I run a permission repair, and everything goes back to normal for a little while, then one day *bang* it starts again.

Has anybody else experienced something similar, or does anybody know if there's a way that I can track specific files' permissions modifications so I can see exactly what the culprit is?  I have a great deal of software installed via homebrew and non-MAS avenues so I think it'd be pretty complicated to track it down exactly, any tips are greatly welcomed.
I don't know if the permission issues are related, but revealing files in Finder not working and Archive Utility stopping to respond are both symptoms of the Apple Events bug that was introduced in 10.8.2.

I don't know if it was fixed in 10.8.3, but when that starts happening, you can terminate appleeventsd from Activity Monitor or with sudo killall -9 appleventsd (without -9 other processes stop responding for some reason). The issue will probably return within a few hours or days though.