Disappearing window borders after reboot
Sometimes this problem shows up to me too. I found out a workaround for this. If you have the Compiz Fusion Icon installed (package fusion-icon) you can click on it with the right button and then click on the 'Reload Window Manager' option. This always works for me.
Sure it's not the solution for the problem, but it might help you until it gets fixed. And I'm sure there is a command which reloads the window manager without having to install the fusion icon, but I don't know it. If anybody knows the command please post a comment.