However, some of the cheques issued by gox have dirt on them. Some customers cleaned the cheque first, then sent to Bitcoin Bank and got paid. The related gox bank account is then emptied.
One important point here is that this all was fine, as long as banks accepted both dirty and clean receipts, and dirty receipts issued by gox were actually more likely to reach the bank, because all receipts are sent by post, and it would take significant amount of effort for the customer to intercept those receipts and modify them.
But at some point banks have changed their policy and decided not to accept dirty receipts to prevent exactly this form of of fraud - modification of receipts. There are many ways to produce dirty receipt, but only way to produce clean. So they rejected them and simply throw dirty receipts away. And that's when some customers were able to collect those rejected recepts, clean them and re-submit to make them processed (unnoticed by Gox).
There is still exist a hypothetical problem of malicious banks, but it has very low impact, and will be addressed in the future bitcoin releases.