Ubuntu 11.10 64bit (upgrade from 11.04 some months ago), System up-to-date. HP 6715b 4GB Ram
Sometimes hitting [Esc] will fix it on some foreground windows.
It never shows over System Settings, background or desktop icons (which do flash a highlight as it passes over)
Right now, it shows inside this FF window & FF tabs, but not FF top window status line (name & max/min/close icons) unless I left-click, when grab-hand appears. It rapidly changes from visible to invisible as it travels along the left & right edges of the FF window(the 'resize' icon flashes visible to invisible and back to visible as it traverses the border, ending up invisible over the desktop.
I've changed the System Settings - Appearance - Theme a few times without fixing it.