The file permissions would have gone wrong, due to the following reasons?
1. You would have not set the umask -22
2. Your initial file permission settings before the install on the directory would have been set wrong.
Most of the times it would be the case 1. Be carefull when you reset the permissions as some of the files are read only. My bet would be to wipe out every thing and follow the manual and reinstall.
Comming to the question of two files with 0, it was because they are older versions of the executables at times required.
Life is a journey, not a destination!