After updating my Ubuntu 16.04 I experienced the same issue. I solved it by removing the
rm -rf /home/your_username/.config/compiz-1/compizconfig
After which I logged out and in.
The directory originally contained the files:
After removing the directory and logging in and out, it now contains the files:
done_upgrades file has not changed and the
config file has changed from:
backend = ini
integration = true
plugin_list_autosort = true
profile = unity-lowgfx
s0_outputs = 1488x858+0+0;
So I guess the issue was caused by one of these files, but I know nothing about compiz, so I cannot tell what could have caused it.