Hi Victor, May be any reason of below mention, since it is be not clear from your question the exact reason.

1. Kindly be sure if you are selecting the right account (from COA) for your invoice and for customer Rec. and Income account , while for supplier Payable and expense accounts respectively.
2. Invoice total is coming the total balance which need to be paid,
3. Are you not selecting the partial payments on your invoice amount.

First have a look all these conditions n then let me know if there is some other problem.

Thanks.