After testing, i'm going to revising my previous comment,
The truth is,
Package - Lock Version on Synaptic is only works for Synaptic only.

To prevent upgrading version by apt-get upgrade and Update Manager,

        echo "squid3 hold" | sudo dpkg --set-selections

After doing that apt-get upgrade, is saying

        The following packages have been kept back:
          squid3

Update Manager is still showing squid3 but it's uncheckable

Well this satisfy me.. \(^ ^)/

Note:
1) To cancel holding version, i'm using 
        echo "squid3 install" | sudo dpkg --set-selections
2) I found really usefull infos here, 
http://askubuntu.com/questions/18654/how-to-prevent-updating-of-a-specific-package

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https://bugs.launchpad.net/bugs/744879

Title:
  apt-get dist-upgrade is overwriting compiled packages

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