Unreadable nautilus and thunderbird in gnome session, please see screenshot

I have the same problem for about a year and could not find a permanent solution. There is a simple, temporary solution: If you change the "Antialiasing" option of the Fonts to "None", the characters will re-appear. You can use (Unity) Tweak Tool to do so. The next time you log in, you can switch "Antialiasing" to RGBA or Grayscale until you have the same problem.