The more I read the more I think the problem is the ball valve breather as you say acting as a pump . A gearbox breather should not be one way. I can understand the swan neck pipe, that makes sense , but if you stick a one-way valve on it this just won't work. I have a theory as to why it is not as bad or no leak on some cars fitted with the modified breather. Maybe some cars have a breather without the ball valve , they would look the same on the outside but would operate differently. Just my thoughts.