If anyone signed up for this promotion through ebay you have to call them to put your user id on their list to get reimbursement for fees.
Apparently there is a bug in the FVF refund part. I had about $5k in promotion sales that were suppose to get 4.5% refund. Ebay did not set it up to be automatic but to be done within 30 days of the sale. It is a known site bug, but the vibe I got from my rep was that they were only looking into the issue for accounts that call in. There was also no ETA on when it would be resolved.
With the promotional sales tools that are set up, it would take less than a minute to calculate the refund so I am not sure what the issue on this is.