Hi,
We had to switch to the newest API to get any shipping information after eBay discontinued the one that we were previously utilizing. The new API currently does not provide transaction information for shipping paid for with bulk shipping, which initially caused the bug you mentioned where it returned the entire bulk shipping purchase for each shipment in that bulk purchase. We have a support ticket in with ebay developer support team, and they are working on the issue, but in the mean-time, we manually cut off the obviously incorrect bulk shipping information from returning in the download.
The expectation is that we will have a resolution on this within a reasonable time frame, and you will be able to reset your download duration and recover all of the incorrect and missing shipping information.
I hope that helps explain the current status with the new shipping API. Let me know if you have any more questions or concerns.