You posted in a comment that you are working on a Mac OS X system. This is an important clue to the purpose of these ._* files.
These ._* archive entries are chunks of AppleDouble data that contain the extra information associated with the corresponding file (the one without the ._ prefix). They are generated by the Mac OS X–specific copyfile(3) family of functions. The AppleDouble blobs store access control data (ACLs) and extended attributes (commonly, Finder flags and “resource forks”, but xattrs can be used to store any kind of data).
The system-supplied Mac OS X archive tools (bsdtar (also symlinked as tar), gnutar, and pax) will generate a ._* archive member for any file that has any extended information associated with it; in “unarchive” mode, they will also decode those archive members and apply the resulting extended information to the associated file. This creates a “full fidelity” archive for use on Mac OS X systems by preserving and later extracting all the information that the HFS+ filesystem can store.
The corresponding archive tools on other systems do not know to give special handling to these ._* files, so they are unpacked as normal files. Since such files are fairly useless on other systems, they are often seen as “junk files”. Correspondingly, if a non–Mac OS X system generates an archive that includes normal files that start with ._, the Mac OS X unarchiving tools will try to decode those files as extended information.
There is, however an undocumented(?) way to make the system-supplied Mac OS X archivers behave like they do on other Unixy systems: the COPYFILE_DISABLE environment variable. Setting this variable (to any value, even the empty string), will prevent the archivers from generating ._* archive members to represent any extended information associated with the archived files. Its presence will also prevent the archivers from trying to interpret such archive members as extended information.
COPYFILE_DISABLE=1 tar czf new.tar.gz …
COPYFILE_DISABLE=1 tar xzf unixy.tar.gz …
You might set this variable in your shell’s initialization file if you want to work this way more often than not.
# disable special creation/extraction of ._* files by tar, etc. on Mac OS X
COPYFILE_DISABLE=1; export COPYFILE_DISABLE
Then, when you need to re-enable the feature (to preserve/restore the extended information), you can “unset” the variable for individual commands:
(unset COPYFILE_DISABLE; tar czf new-osx.tar.gz …)
The archivers on Mac OS X 10.4 also do something similar, though they use a different environment variable: COPY_EXTENDED_ATTRIBUTES_DISABLE
I'm not sure Tar can do that. It should be possible, though, to untar both backups (to different directories), then use something along the lines of
cd /mnt/oldbackup ;
find ./ -exec getfacl {} | setfacl /mnt/newbackup/{}
as the output of getfacl can be used as stdin for setfacl according to the manpage.
Best Answer
That's up to the root who unpacks:
If you want to make them all root to start with, you can use