If we use the getString() method to get the value from a ResultSet for a integer column with the zerofill option the value we obtain doesn't have the expected leading zeros.
We can reproduce the behavior with the next snippet:
{
Connection connection = DriverManager.getConnection (connectionString, user, password);

Statement st = connection.createStatement();
st.executeUpdate("drop table if exists tmpTest;");
st.executeUpdate("create table tmpTest (id int unsigned primary key auto_increment, value smallint(3) unsigned zerofill not null unique);");
st.executeUpdate("insert into tmpTest(value) values (1), (4), (5), (8);");

PreparedStatement pst1 = connection.prepareStatement("select value from tmpTest");
ResultSet rs1 = pst1.executeQuery();
while(rs1.next())

{ System.out.println("Value: " + rs1.getString("value")); }

rs1.close();
pst1.close();

st.close();
connection.close();
}

Using the 1.1.8 or 1.2.3 versions of the connector this returns the expected result:
Value: 001
Value: 004
Value: 005
Value: 008

In any version after 1.3.0 the behavior changes:
Value: 1
Value: 4
Value: 5
Value: 8