Programs run in full screen while using xfwm4 (without composite in use) are covered by xfce4-panel.
Using metacity before running a fullscreen app is one known work around.
I am using Nvidia 180.29 drivers (always find it helps to mention this :) ) Using only Xfce Menu, task list, clock and notification area panel plugins.
Can you give a bit more details on how do reproduce this, be cause it is not how it is supposed to work, and I obviously cannot produce that.
Fullscreen apps are set back to their original layer when they loose focus.
Starting with what application, how you switch to fullscreen (Alt-F11 or application option) and the output of "xprop" on the application window that is covered by the panel.
Oh, and also the output of "xfwm4 --version", that always help clarifying what version of xfce/xfwm4 you run...
To reproduce this, open Google Chrome and go fullscreen. Switch to a different workspace and go back; the panel will cover Google Chrome. As a temporary solution, I enable window compositing and check the option to display fullscreen windows directly.
similar to 8563
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