It certainly is ! 
It would be a good idea if you filed a bug here:
https://bugs.launchpad.net/ubuntu-mate
Probably because what is called a "race condition".
The start of the panel should be delayed until compiz is up and running.
As a workaround you can automate the restart of the mate-panel, you can create a new item in "startup applications" and use the command "mate-panel --replace", also set the delay at 3 seconds or something like that. This makes sure compiz is ready before the panel starts.
Also check in CCSM if mate-compatibility is enabled , you might want to do a "reset CCSM" first.
AFAIK the Window key is the Super key but the keybindings in compiz differ a lot from the keybindings in marco. You might want to customize that in CCSM also check if there are no conflicts between the keybindings.