Just turning off notification of updates will not be enough. There are several background jobs that run apt-get update (including a nightly cron job if I remember right).
To stop the pop-up run
Then in settings, set Update automaticly to 'Never' and Notify of new version to 'Never'
I suggest leave security at immediately and, setting "others" to every two weeks.
You also need to make sure your not running apt-get update anywhere else. This can happen when you install software, run update-manager, or in a cron job.
If that doesn't work for you:
You can do this by
/etc/apt/apt.conf.d/10periodic and changeing
You can always
apt-get remove update-manager-core to remove the feature all together.