New iTunes MAY Cause Problems

One of our members downloaded the latest version of iTunes and then lost a lot of files including their iPhoto library and the ability to Repair Permissions. 

After extensive research, they determined that new iTunes was the problem. 

So they trashed iTunes and the Repair Permissions worked. Then they downloaded iTunes again and set it up on the computer. Just for the heck of it, they ran the Repair Permissions again and it FAILED!  
They then checked the Apple Knowledge Base for complaints and found many of these type of problems. Apparently, the new iTunes is causing problems, specifically the problem of interfering with Repair Permissions.