Sorry for the delay in replying to you.
A support call has been created for you, the call reference number is F0056664.
Can you please send to us via e-mail, a copy of the table creation script from each data source. The columns you have selected to be the custom comparison key and screen shots of the behaviour you are seeing.
Hopefully we will be able to provide an answer to you. Please send the e-mail to firstname.lastname@example.org
and include the above call reference number in the subject field on the e-mail.