Hi Hans,
Does the login screen display an error, when attempting to SSO through the URL? If so, what does it say? I would run a setspn -l <Service-Account-Name> to ensure that everything is setup properly. I've had an issue before where I forgot to add a line and it had me stumped for a while, it could be that simple.
In either case, I would suggest running an HTTP trace tool, such as Wireshark, in order to see why the SSO trust isn't occurring. If it's working for the server name and not the URL, something isn't delegating right between Windows AD & the backend BusinessObjects servers.
One other thing, I dug around the SAP Marketplace, to see if I could find a note. What browsers are the users utilizing? If it's Chrome, this note (https://service.sap.com/sap(bD1lbiZjPTAwMQ==)/bc/bsp/sno/ui_entry/entry.htm?param=69765F6D6F64653D3030312669765F7361706E6F7465735F6E756D6265723D3138383731393326, may prove valuable to you. I know you have a lot of users, however, you can deploy this change through a group policy update and the end users will never know. I know you're looking for a server side solution, but this can be a temp one, until a server-side solution is found.
If you need help digging through the Wireshark log, just let me know and I'll be glad to help you out with it. Thanks,
-Victor