Hi,
problem here is that TDP compare data based on position of data. We expect that key columns are almost same and we don't do any sophistic join between tables. Because data 2 and 3 are not in same position (or in next row) after we ordering tables then we are not able pair these rows for compare.
I am thinking about one more complicated solution. If you don't need generate script you can use specific select statement and compare results. You can join your tables in Cross-Connection Query Builder and get results from tables. Then you are able compare these two Grids and see differences. It is not so elegant solution but maybe should help you.
Filip