Following your description, I made an example to try to duplicate the behavior you were describing.

However, it does not do what you say. It seems to work fine.

#!/usr/bin/perl -w
use DBI;
use strict;
package One;

sub new {
    my $class = shift;
    my $self = bless {}, $class;
    my $dbh = shift || return undef;
    $self->{dbh} = $dbh;
    return $self;
}

sub execute {
    my $self = shift;
    my $query = shift;
    my $sth= $self->{dbh}->prepare($query);
    my $rows = $sth->execute or die $DBI::errstr;;
    print "$rows rows affected\n";
}

sub begin_work{
    my $self = shift;
    $self->{dbh}->begin_work;
}

sub commit{
    my $self = shift;
    $self->{dbh}->commit;
}

package Two;

sub new {
    my $class = shift;
    my $self = bless {}, $class;
    my $dbh = shift || return undef;
    $self->{dbh} = $dbh;
    return $self;
}

sub execute {
    my $self = shift;
    my $query = shift;
    my $sth= $self->{dbh}->prepare($query);
    my $rows = $sth->execute or die $DBI::errstr;;
    print "$rows rows affected\n";
}

package main;

my $dbh= DBI->connect("dbi:SQLite:dbname","","",{RaiseError => 1,AutoC
+ommit=>1})
#my $dbh = DBI->connect("DBI:mysql:dbname",
#    'user', 'password', {RaiseError => 1, AutoCommit=>1})
    or die "can't connect\n";

$dbh->do(qq{delete from table1 where t2id =5});
$dbh->do(qq{delete from table2 where t2id =5});
my $query = qq{ insert into table1 values (5,"xxx") };
my $one = new One $dbh or die "can't create One\n";
my $two = new Two $dbh or die "can't create Two\n";
$one->begin_work();     # transaction starts in module One
$one->execute($query);  # transaction continues in module One
$query = qq{insert into table2 values(11,"yyy", 5)};
$two->execute($query);  # transaction continues in module Two
$one->commit();         # transaction ends in module One
$dbh->disconnect();
[download]

I tried this example with two different DBD drivers (MySQL and SQLite) and it worked as I expected. The transaction is processed correctly. Try to add a call to $dbh->rollback() after the first execute, and it will cancel the insertion without problems. It means that the transaction is really split across packages.