Hey community! Thanks to your feedback I solved the issue, following further steps:
1) Removed all eclipse installations from my Ubuntu;
2) Uninstalled KDS (sudo aptitude purge kinetis-design-studio);
3) Removed $HOME/.eclipse directory
4) Removed KSDK1.2 (I've installed it on /opt/Freescale/)
5) Removed the directory /opt/Freescale
6) Re-Installed kinetis-design-studio (sudo dpkg -i kinetis-design-studio-3.0.0-amd64.deb)
7) After installation, changed the directory owner to me (a.k.a. ronaldo) (sudo chown -R ronaldo:ronaldo /opt/Freescale)
8) Opened KDS and updated it (Help->Check for Updates->next next finish)
9) After update, closed KDS and extracted KSDK to /opt/Freescale
10) Added KSDK Updater to KDS (Help->Install new software...)
After those 10 steps all worked as expected!
Thank you!