Hi,
You have, first of all, to see what type of commitment items participate in the payment process and check if their financial transactions correspond to the eligible combinations described in the note.
Second, you have to check what S200 you use: is it enhanced or simple one. Keep in mind, that there are numerous OSS notes which rectify different cases with this program and some of them are quite recent. So, you have also to check that your SAP release (what is it, by the way?) is adequate in this perspective.
Unfortunately, long-distance analysis of S200 performance is practically impossible, under assumption that all other settings, I mentioned above are 'descent'. It is essential to see the data and sometimes debug the program to understand why it does not 'catch' this or that document.
Regards,
Eli