I have the same problem. I found that if I don't upgrade VMWare tools in a Windows 7 VM after upgrading to Fusion 13, Unity mode works properly. If you make the mistake of upgrading Tools, there is no way of going back to a previous version. I tried, it keep reinstalling the current version after I downloaded and tried to install a previous version of tools.
Hopefully this gets fixed in a future release as it is really annoying!
