Hidden files & folders after executing Killall Finder command

This little ditty might help...

for ff in '/Network /Volumes /bin /cores  /etc 
  /mach /mach_kernel /private /sbin /tmp /usr /var '
do
   sudo chflags hidden $ff
done

You'll want to add in /opt if you added that and any other non-standard directories in / you wish to hide from the GUI.

As to why - you might need to track that down using fs_usage, but typically it's an installer that brute forces permissions or otherwise removed the metadata flags from those files.

Hallelujah! I figured it out. Okay, so first thing I did was create a new account, as suggested by another answer. The problem did not occur in there, so clearly the problem was limited to my account. I then went into Safe Mode into my account. The problem did not occur as well. So clearly something was loaded in normal mode but not in safe mode that was causing the problem.

While in safe mode, I then cleared the caches (in Terminal, using sudo mv /Library/Caches ~/Temp/ and the same for ~/Library/Caches). Problem solved! I've had other problems as well in Finder so perhaps this will fix this as well. I'm curious as to why using Onyx to clear the User caches didn't clear these as well, but anyway, from what I've read online it seems like getting rid of these two folders is safe. Also, Time Machine never backs up ~/Library/Caches (but it does back up /Library/Caches), so that's reassuring.

In addition, while this post was made in 2003, it still applied to my situation and this was what convinced me to clear my Caches folders.