Maybe this can help;
Make sure your using the same Virtualbox version as the Guest Additions. 6.1.2. The Guest Additions have recently been upgraded by the Whonix team, so you do not have to do anything with that. As long as your Virtualbox version on your host machine is 6.1.2 or higher, the clipboard will work. In the Virtualbox gui on the host, remember to tick the box Settings–> General, and in the “Advanced” tab 2 options: shared clipboard and drag and drop.
Also, if you have not already, update your Whonix machines:
sudo apt-get update && sudo apt-get upgrade
Also, if you have any other guest additions package installed, remove it because you do not need it.