Each time I closed a Cubase’s project it didn’t close main windows … 
It seems like it depends on the size of the project and it could be sometimes very long if it’s a big project …
It can also be a third party plugin that causes this.
Do you use Waves plugins? I have this same problem and sometimes cubase freezes on startup while scanning Vst3 plugins. I found that the probleme was caused by some files named ‘waveShell’, when i removed them from the Vst3 folder the issue doesn’t occurre anymore… when i put them back in the Vst3 folder i encountred the same problem… i sent an email to waves support and i am waiting for their replay…
hope this can help you find the source of the trouble…
I’ve found that sometimes it just takes very long depending on the project. But I have also found some success in opening and saving a smaller file if you’re having trouble with another file not closing and sometimes that makes a difference. Then sometimes a certain file just won’t close at all. Just odd behaviour.
Waves support gave me all the necessary help to resolve the issue. I highly suggest everyone having Waves plugins and experimenting problems launching or closing cubase to contact Waves support (absolutly great support if not the the best i’ve ever meet!)
Hey. Glad you got it figured out. However, it would be helpful if you posted your solution, even if the support people is very helpful.
Yes do tell, it may be useful for lots of people on this forum!
Hi,
The fix was to uninstall all the waves plugins including the Waves central, then to delete all the waves files from several folders…then to reinstall all the pluggins…but this didn’t worked for me, so the waves support remotely connect to my computer and look into this issue…the was problem was with the license location…
Aha. So many things that can go wrong. 
Thanks for sharing dude.