Time Machine hasn't been backing up the full system since before 10.8.3
You aren't supposed to browse the Time Machine directory tree directly. Try entering Time Machine from the Finder and just look for those folders from there.

If you're sure that those folders aren't in the backup, check System Preferences -> Spotlight -> Privacy.
To check all the excluded items, you can execute this command from Terminal:

sudo mdfind "com_apple_backup_excludeItem = 'com.apple.backupd'"


It will display a list of excluded paths.
If you can't identify the source of the issue, I suggest to wipe the backup drive and to make a new backup.