Maybe buffering is confusing your debugging efforts?

#!/usr/bin/perl --

use strict;
use warnings;

Main(@ARGV);
warn "\nCommencing GLOBAL DESTRUCTION PHASE";
exit(0);

sub Main {
    {
        my $mya = MyA->new;
        my $myb = MyB->new($mya);
        my $myc = MyC->new($mya);
        undef $mya;   
    }
    warn "\nstill in Main";
    my $myc;
    {
        my $mya = MyA->new;
        my $myb = MyB->new($mya);
        $myc = MyC->new($mya);
        undef $mya;
    }
    warn "\nReturning from Main";
}

BEGIN {
    package MyParent;
    sub new     { my($c)=shift; bless {@_}, $c }
    sub DESTROY { warn "DESTROY @_ "; }
    $INC{'MyParent.pm'}=__FILE__;
}
BEGIN {
    package MyA;
    use parent qw' MyParent ';
    $INC{'MyA.pm'}=__FILE__;
}
BEGIN {
    package MyB;
    use NEXT;
    use parent qw' MyParent ';
    sub new { shift->SUPER::new( MyA => @_ ); }
    sub DESTROY {
        warn "BREAK LEAK @_ ", delete $_[0]->{MyA};
        $_[0]->NEXT::DESTROY;
    }
    $INC{'MyB.pm'}=__FILE__;
}

BEGIN {
    package MyC;
    use parent qw' MyParent ';
    sub new { shift->SUPER::new( MyA => @_ ); }
    sub DESTROY {
        warn "LEAK @_ ", $_[0]->{MyA};
        $_[0]->NEXT::DESTROY;
    }
    $INC{'MyC.pm'}=__FILE__;
}
__END__
LEAK MyC=HASH(0xa47114) MyA=HASH(0x3f8d4c) at - line 56.
DESTROY MyC=HASH(0xa47114)  at - line 31.
BREAK LEAK MyB=HASH(0x9c9864) MyA=HASH(0x3f8d4c) at - line 45.
DESTROY MyA=HASH(0x3f8d4c)  at - line 31.
DESTROY MyB=HASH(0x9c9864)  at - line 31.

still in Main at - line 17.
BREAK LEAK MyB=HASH(0xa47174) MyA=HASH(0x9c9864) at - line 45.
DESTROY MyB=HASH(0xa47174)  at - line 31.

Returning from Main at - line 25.
LEAK MyC=HASH(0xa47124) MyA=HASH(0x9c9864) at - line 56.
DESTROY MyC=HASH(0xa47124)  at - line 31.
DESTROY MyA=HASH(0x9c9864)  at - line 31.

Commencing GLOBAL DESTRUCTION PHASE at - line 7.
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