What version of Blesta are you using? It may be best to upgrade to version 3.5.2 as there were a couple changes to Blesta that can affect non-merchant gateway payments. One is whether an error transaction is recorded when Blesta receives an invalid response (CORE-1747), and another is the addition of currency precision to resolve issues where minute price differences would cause an invoice not to be paid (CORE-1742), similar to what you've described.