Opt / Private Folder visible on HD?
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.