I had the same problem. I am using Python and Eclipse on Windows. The code was running just fine, but eclipse show errors everywhere. After I changed the name of the folder 'Lib' to 'lib' (C:\Python27\lib), the problem was solved. It seems that if the capitalization of the letters doesn't match the one in the configuration file, this will sometimes cause problems (but it seems like not always, because the error checking was fine for long time before the problems suddenly appeared for no obvious reason).