You could still have one of the IPs that don't have a license. Check the warnings when you compile your design. Two other possibilities come to mind:
- If you have a floating license on a network and if someone else is using the license at the same time than you, in some cases the compilation will fail and in some other cases it will continue but generate a time limited .sof. Again it will show as a warning. You can preventthis behaviour by checking the 'wait for license' box in the license setup window.
- If you have an SOPC system in your project, don't forget to regenerate it once you have the licenses. If you don't the final .sof file will still be time limited.