First, a few code comments:


0) (Update:) Doh--i missed one of the first and foremost things-- add use strict; and use warnings; !!!
1) For this, check perldoc -f localtime:

my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(t
+ime);
$date = "$mday/$mon/$year $hour:$min:$sec"; # THIS IS WRONG!!!!

# do something like this instead:
my @time = localtime;
my $date = sprintf("%2d/%2d/%4d %02d:%02d:%02d", $time[4] + 1, $time[3
+], $time[5] + 1900, @time[2,1,0]);
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2) This (look at perldoc -f exists):

while(my ($key, $value) = each(%forward)) {
    if ($to =~ $key) {
        $local_address = $key;
        $forward_address = $value;
    }
}
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should be replaced with:

if( exists $forward{$to} ){
        $local_address = $key;
        $forward_address = $value;
}
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3) Use (see DBI docs) heredocs and placeholders. (Also, i believe this 'LEFT JOIN' should be just 'JOIN')

    $sql = <<EOF;
SELECT "tblForwardMail"."ForwardMailID", "tblFilterMail"."FilterMailEm
+ail"
            FROM "tblForwardMail"
            LEFT JOIN "tblFilterMail" ON "tblForwardMail"."ForwardMail
+ID"="tblFilterMail"."ForwardMailID"
            WHERE "tblForwardMail"."ForwardMailTo"=?
EOF
#    $sth = $dbh->prepare($sql);
#    $sth->execute( $local_address );
#    while (@row = $sth->fetchrow) {
#        push(@filter, $row[1]);
#    }
#
# But it seems like what you want next is just:
(undef,$filter_address) = $dbh->selectrow_array($dbh,{},$local_address
+);
# make sure to pre-declare $filter_address
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4) This:

foreach my $email_address(@filter) {
    if (($from =~ $email_address)){
        $store = "YES";
    }
}
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could be:

$store = "YES" if grep( $_ eq $from, @filter );
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but if you use my comment #3, then it's just:

$store = "YES" if $from eq $filter_address;
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BUT, you should treat $store as a boolean and give it true (1) and false (0, undef) values, so you don't have to string match 'YES' later..

  $store = 1;  # true
  $store = 0;  # false
  if( $store ){
    ...
  }
  if( ! $store ){
    ...
  }
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5) This:

#Declare variables to be used including command line variables if need
+ed
my ($stored_email, $log, $to, $from, $forward_address, $store, $body, 
+$sql, $sth, $date, $local_address);
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is "c-ish" .. here it's usally better to declare stuff just when it's being used (especially if it only exists in a limited block/scope)

---

gotta cut back to work for a moment ;) but then i'll go back and see if can find the bug..