Restocking fees

We ship a couple thousand orders a day and in return get a couple dozen returns daily. We do charge a restocking fee if the item comes back used and cannot be resold as new. Amazon will allow us to upload a photo, charge a restocking fee, and issue a partial refund. However, we find that every time we do this, the following day when checking the order, there is no refund being shown as ever being issued. We have to repeat the process all over again. After doing this a second time, it is finally successful. Is anyone else having this issue?