Geeza, let's see if I get this correctly.
You have an installation in which "/" is using 12 Gb, and "/home" is using 9.8 GB; both partitions with extra spare space.
You then made a remaster of this installation using MyLiveCD.
Then you installed this remaster in a new system.
In this new system, "/" is showing only 6 GB used, and "/home" is showing 9.4 GB used.
Is this correct?
Then, nothing is wrong.
When you make the remaster, the script intentionally leaves out several folders, like "/var/cache", "/tmp", "/root/tmp", to mention a few. These folders have data that is temporal or relevant only to the particular installation, and you don't want them transported to a new, fresh installation.
In some cases, this data can be pretty large. For example, under some conditions you can have a lot of downloaded packages in "/var/cache/apt". Also, the thumbnail cache can be pretty big very easily.
So don't worry, if you used the MyLiveCD as usual, nothing is missing; all that was left out were temporal data that you don't need in a new install.
Hope this clarifies your doubt.