I have found a work-around effective even though the Compiz is running.

The principle (for  M$ Windows running in the seamless mode under
VirtualBox):

"As long as you keep some M$ Windows application window open you can
minimize and restore other Windows applications without any problems
with their proper redrawing. "

To reproduce that you may try and install e.g. the following little analog 
clock into your Windows virtual machine:
 http://www.gljakal.com/clock/index.php
The clock will stay running and visible on the Gnome workspace where you have 
the seamless desktop. An all other apps windows will work right.

Perhaps, this can also help to track where this bug has its cause.

-- 
virtualbox does not redraw background in seamless/compiz mode
https://bugs.launchpad.net/bugs/230811
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