If you do an upgrade or a "dirty" install where you do not reformat partition, all the old files including kernels & related files will still be in /boot and probably in /usr/src but not in dpkg as current system did not install them.
This will only show those still in dpkg.
dpkg -S /usr/src/*
ls -l /usr/src
cd /boot
ls -l /boot
Always best to use dpkg, apt-get or synaptic if registered as part of install.
If you just use nautilus to delete using gksudo, then you may have just moved them into root's trash. And sometimes housecleaning root's trash can be an issue.
How To: Disk Full? - Check Your Trash
http://ubuntuforums.org/showthread.php?t=898573
And then you may have lots of very old log files and other left over bits.
RecoverLostDiskSpace
https://help.ubuntu.com/community/RecoverLostDiskSpace



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