Im having really weird issue going on with unity desktop. As you can see on screenshot my main monitor(on left) is having panel solid black and my secondary monitor(on right) is having properly transparent panel. In CCSM I've set Opacity to 0, I tried executing 'unity' command but that did not help.
I was able to solve this using following commands
unity-tweak-tool --reset-unity dconf reset -f /org/compiz setsid unity
First command is reseting all settings back to default in unity-tweak-tool, second command is reseting compiz to default and finally last command is restarting unity.