How safety is Ubuntu Tweak Janitor for system?

How safety is Ubuntu Tweak Janitor for system?

I had some trouble with Tweak Janitor.
I cleaned my system with all checkboxes that was available.
After cleaning when I restarted PC I caught to text terminal it's all, smt:
Ubuntu 12.04.3 LTS nazar-desctop tty1
nazar-dezsctop login: // I typed correct login + password
nazar-dezsctop password:
and after log in next info:
7 packages can be updated
7 updatees are security updates
I got out from this trouble by next steps:
Stop LightDM with sudo stop lightdm
Install GDM with sudo apt-get install gdm
Start GDM with sudo start gdm
Run sudo dpkg-reconfigure lightdm to set the default display manager for gdm
Restart computer and login.
I wondering to know about safety usage of Ubuntu Tweak Janitor.
Question:
For example what happen if I'll try to use it again in the future?
If I had use LightDM what would happen?
Why ubuntu didn't tall me about these updates after cleaning?