Perhaps you should post some example code that shows your problem. I coded up a simple test that shows DESTROY() being called, as I'd expect.

# debug_test_DESTROY.pl

package Foo;

my $i;

sub new {
        return bless [++$i]
}

sub DESTROY {
        warn "destroying object <$_[0][0]>\n";
}

package Main;

$x = Foo->new;
$y = Foo->new;

print "hello";
[download]

> perl -d debug_test_DESTROY.pl

Loading DB routines from perl5db.pl version 1.28
Editor support available.

Enter h or `h h' for help, or `man perldebug' for more help.

Foo::(debug_test_DESTROY.pl:3): my $i;
   DB<1> n
Main::(debug_test_DESTROY.pl:15):       $x = Foo->new;
   DB<1> n
Main::(debug_test_DESTROY.pl:16):       $y = Foo->new;
   DB<1> n
Main::(debug_test_DESTROY.pl:18):       print "hello";
   DB<1> q

destroying object <1>    ## <--- look, DESTROY() called for $x ##
 at debug_test_DESTROY.pl line 10
        Foo::DESTROY('Foo=ARRAY(0x97acc6c)') called at debug_test_DEST
+ROY.pl line 0
        eval {...} called at debug_test_DESTROY.pl line 0

destroying object <2>    ## DESTROY() called for $y ##
 at debug_test_DESTROY.pl line 10
        Foo::DESTROY('Foo=ARRAY(0x97f1348)') called at debug_test_DEST
+ROY.pl line 0
        eval {...} called at debug_test_DESTROY.pl line 0
[download]