I quickly ran a test that creates 3 hashes of the type and depth that you mentioned. Here's the ps command output:

  PID TTY      STAT   TIME  MAJFL   TRS   DRS  RSS %MEM COMMAND
22842 pts/1    R+     0:00      0    10  6941 1680  0.1 perl xxx.pl
create all the hashes
  PID TTY      STAT   TIME  MAJFL   TRS   DRS  RSS %MEM COMMAND
22842 pts/1    S+     0:23      2    10 932137 883884 85.5 perl xxx.pl
clean out hashes
  PID TTY      STAT   TIME  MAJFL   TRS   DRS  RSS %MEM COMMAND
22842 pts/1    R+     0:30     31    10 932137 885632 85.6 perl xxx.pl
we're done
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Memory requirements of your program are likely to be at least 933 MBytes this is without DBI etc.!! Since you mentioned that your computer has 1GByte internal memory on board the sheer size of the hashes definitely will require the operating system to swap memory pages.
The Perl garbage collection is not the cause of this problem, even while it does require some time. The operating system takes time to memory swap things in good shape again.
So you may want to add a bit more internal memory to your system to run an application like this one ;-)

Test-program source:

#!/usr/bin/perl
use strict;use warnings;

sub showtime {
    print `ps -p $$ v`;
    }

showtime;
print "create all the hashes\n";
my %h1;
foreach my $one (0..64000) {
   $h1{$one}={};
   foreach my $two (0..2) {
      $h1{$one}{$two}='foo';
      }
   }

my %h2;
foreach my $one (0..2200000) {
   $h2{$one}={};
   foreach my $two (0..3) {
      $h2{$one}{$two}='foo';
      }
   }
my %h3;
foreach my $one (0..1) {
   $h3{$one}={};
   foreach my $two (0..1) {
      $h3{$one}{$two}={};
      foreach my $three (0..1) {
         $h3{$one}{$two}{$three}={};
         foreach my $four (0..9) {
            $h3{$one}{$two}{$three}{$four}={};
            foreach my $five (0..14) {
               $h3{$one}{$two}{$three}{$four}{$five}={};
               foreach my $six (0..39) {
                  $h3{$one}{$two}{$three}{$four}{$five}{$six}='bar';
                  }
               }
            }
         }
      }
   }


showtime;
print "clean out hashes\n";
%h1= ();
%h2= ();
%h3= ();
showtime;
print "we're done\n";
[download]