We could better help you if you showed us the actual code you used with extractMember and addFile. When I use those, it works fine.
use Archive::Zip qw( :ERROR_CODES :CONSTANTS );
# Include actual filenames in the next three lines
my $oldfile = 'oldzip.zip';
my $newfile = 'newzip.zip';
my @wanted = ( 'perl.log', 'perld.log' );
my $oldzip = Archive::Zip->new();
$oldzip->read( $oldfile ) == AZ_OK or die 'read error';
my $newzip = Archive::Zip->new();
for my $file ( @wanted )
$oldzip->extractMember( $file );
$newzip->addFile( $file );
$newzip->writeToFileNamed( $newfile ) == AZ_OK or die 'error somewhere
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