Ok, so this occurs at the end of the freeze process, after the progress indicator reaches 100%.
When you reopen the project it is obviously the last saved version and therefore the freeze has not been applied.
However, if I search the project folder, I find the file has been created and can be opened and listened to.
There are no disabled tracks in the project and render in place works as expected.
I realise I could use render in place as a substitute however freezing has some distinct advantages so I’d prefer to use that.
My system - Cubase Pro 9.0.20, Windows 10 Home 64, AMD FX-8150, AS Rock motherboard, 16gb RAM
One interesting point is this. I had the exact same issue with Cubase 8, however, that was on a different machine running Windows 7 Ultimate.
I knew I was upgrading and thought that doing so would rectify the problem. Unfortunately this was not the case.