I'm pretty sure it is related to the Changes that you are referring to.
Simple code to play with and check the issue:

#!/usr/bin/perl

use strict;
use warnings;

use Data::Dumper;

my $newConf =  { 'FullKeepCnt' => [ 4 ] };

print "Original structure: ", Dumper( $newConf );

foreach my $var ( sort(keys(%$newConf)) ) {
    my $d1 = Data::Dumper->new([$newConf->{$var}], \[*value]);
    print "\nd1: ", Dumper( $d1 );
    my $value1 = $d1->Dump;
    print "\nvalue 1: $value1\n";

    my $d2 = Data::Dumper->new([$newConf->{$var}], [*value]);
    $d2->Useperl(0);
    print "\nd2: ", Dumper( $d2 );
    my $value2 = $d2->Dump;
    print "\nvalue2: $value2\n";
}
[download]

The output that matters is

value2: @main::value = (
                 4
               );
[download]

whereas the initial arrayref is what BackupPC needs and expects. (The list it gets back now via DumpXS actually ruins BackupPCs config files when using the web interface for editing...)

The pure Perl version returns a list, and so I guess that that's what it should be. My current understanding is that BackupPC did it wrongly for many years, and still does, but was able to get away with it because DumpXS within Data::Dumper was buggy. Now that Data::Dumper is corrected, BackupPCs needs to patch it's code.

Afaict, \[*value] works fine, both with DumpXS and pure Perl. But I'm not fully sure that that's 'the best' patch to be done, even if it works for me.