I think that's somehow related to the specific VM technology that you use, vagrantc also mentioned something about it but I could never reproduce it with VirtualBox.
What VM and which virtual graphics driver are you using? Is your color depth 24 or 32? Does it happen with other color depths?
If we find a quick way to reproduce it, we can then unassign the bug report from epoptes and subscribe x11vnc or xvnc4viewer instead.