According to Brock Wolfe:
Well after more digging found that the files not included in tar archive were tied to hard links. Displayed by find command:
find . -type f ! -links 1 -prinff "%i %n %p\n" | sort -n
I found it almost unbelievable that there'd be such a serious error in tar, but sure enough, it's a known problem...
http://bugzilla.redhat.com/bugzilla/show_bug.cgi?id=63046
Fortunately, it's fixed in Red Hat 7.3 and newer (including rawhide), so you'd just have to get the newer RPM package for tar and update your installed version.
Now I need a solution to cloning a partition that clones hard links correctly.
As long as the file system is not actively being changed, I find that dump and restore work great for cloning partitions, as they preserve just about all the inode information intact. Linus Thorvalds and many of the kernel gurus strongly discourage their use under kernels 2.3.x and newer, but the problem appears to be limited to file systems that are actively being changed, because of the way file information is cached at different levels.