You should repack the directory where you unpacked the original .PAK to; otherwise the relative paths inside the .PAK will be incorrect.
Let's take an example:
Extracting Russian.pak to C:\stuff\ will get you:
PAK Localization\Russian\Fonts\fonts.lsx --> Filesystem C:\stuff\Localization\Russian\Fonts\fonts.lsx
PAK Localization\Russian\russian.xml --> Filesystem C:\stuff\Localization\Russian\russian.xml
[etc.]
When you later repack C:\stuff, the prefix of the paths will be stripped, so you'll get:
Filesystem C:\stuff\Localization\Russian\Fonts\fonts.lsx -> PAK Localization\Russian\Fonts\fonts.lsx
Filesystem C:\stuff\Localization\Russian\russian.xml --> PAK Localization\Russian\russian.xml
... however, when you only repack a *subdirectory*, eg. C:\stuff\Localization\Russian, you get:
Filesystem C:\stuff\Localization\Russian\Fonts\fonts.lsx -> PAK Fonts\fonts.lsx
Filesystem C:\stuff\Localization\Russian\russian.xml --> PAK russian.xml
Notice how the relative paths in the PAK are different; the new package has "Fonts\fonts.lsx" instead of the correct "Localization\Russian\Fonts\fonts.lsx", this is why your package doesn't work.
