Ramon: I guarantee you there is corrosion on the solderable surfaces of your board. The issues are: * Flux selected is capable of removing the corrosion at hand. * Processes for applying the flux and soldering the board are effective for the selected flux.
There are many sources of problems that prevent barrel fill and the corrosion of the solderable surface, that you mention, is but one of them. Among the other sources are: * Corrosion on component leads * Board design * Board fabrication * Soldering process * Etc, etc
What is it about your situation that points you toward corrosion as the cause? Could you take the time to help focus us on: * Specifics of your process * Duration and extent of the problem, both on this product and others