We have the same problem, it would be very nice if magento offered a fix for this. I would have though they would have wanted Customers to run both Magento & Ebay stores - and use PayPal after all they are all owned by the same Company!
Anyway - after a month of waiting here is what I received from PayPal.
Thank you for contacting PayPal Merchant Technical Support.
PayPal does not provide support for custom scripting, but we do have some “as-is” code samples. More than likely, you should just modify your current script to handle only Magento orders, and provide basic validation for all other orders. This is not something PayPal can assist with, and may require you to hire a developer.
IPN code samples
I hope the information that I provided you was helpful. If you have any further questions or concerns about integrating PayPal with your web site, please feel free to reply to this email directly, contact us by phone at: 1-800-852-1973, or go to https://ppmts.custhelp.com/.
So there we are - we just need to modify our script! or HIRE a developer to do it for us - simples!
Any developers out there that can help with the script modification?