I just got a 27" Core i5 with the Fusion Drive and it was doing the same thing - Menu Bar would disappear from screen when I quit any application.
I called Apple, their guy (nice guy, btw) told me to do the following:
- power off/shut down the Mac
- unplug the power cord
- press and hold the power button for about 10 seconds
- plug in the power cord
I did this and the problem was resolved. He said this procedure resets the System Management Controller.
It worked for me - hope it works for you and others who experience this.