Was there any resolution to this problem as I am having the same issue.
To test it out I created an empty project, created 2 audio tracks and recorded 25 seconds of audio (no microphone connected). When I go to the Audio Menu the Open Audio Alignment Panel is greyed out.
I tried opening in Safe Mode with external plug-ins disabled and no preferences options. Not working! I believe I had used this in the past but when I try with a number of different projects I get the same thing.
I’m running Cubase Pro 10.5.20 on Windows 10.
Thanks for any ideas on chasing this down.