I had the same issue and, for a different reason, ended up doing a reinstall. when I reinstalled I opened discover, clicked on settings, and unselected the box for xenial-backports. It will require your password and will notify that a few packages are to be removed, click yes. I did this before installing the initial updates immediately after installation, I do not know if it is necessary to reinstall and do this before initial updates or if it will work anytime. There are 2 xenial-backports sources in my Discover settings, but I only needed to unselect one since the other was not selected by default. The virtual keyboard has not popped up at login any more since I did this.
some menus opened blank after doing this, so I shutdown and rebooted and then all was normal and no more virtual keyboard at login