I've been using Linux Mint in VirtualBox without problems for months, with a gui MATE desktop. The host is a Kubuntu system (using VirtualBox to isolate interactions with the Internet).
Because it interacts with the Internet, I run Linux Mint in a linked clone--should I ever think malware got on the system I can erase the clone and recreate it from its base VM.
Within the past week, I have twice had the linked clone boot into the command line. Both times, startx says xinit isn't installed. When I installed xinit both times, it also found that a multitude of xorg software (xserver.xorg, I think) was missing. I checked against the base VM to which the clone is linked, and xinit and all the xorg software are present. I don't believe I've done anything to erase this software on the clone.
The first time this happened, I installed xinit (and xorg software) on the linked clone and started with startx. A bunch of other software was missing as well--firefox, pluma, the panel was messed up, etc. So, I erased the linked clone, deleted the snapshots, updated the base VM (which I don't use for anything other than creating clones), and created a new linked clone. The new clone worked fine once or twice.
Today the linked clone also booted up in terminal mode and was, again, missing xinit and xorg software. I reinstalled and this time I rebooted the VM. Everything came up fine this time, but having to reinstall my GUI every couple times I use the VM isn't ideal.
Anyone have any ideas as to what is happening here and how it might be fixed? I noticed the problems seemed to have started not long after a recent kernel update (host and guest)--but don't know this is the cause. I also recently started using firejail, but don't see how that could erase software. If it's virtual hard disk corruption, I'd think that recreating the clone from the nearly untouched base VM should have fixed that.