Hello,
I think I am experiencing the same issue at an up to date Jessie amd64 
installation.
There are the nvidia binary driver in use:
ii  kaffeine                                          1.2.2-3                   
         amd64
ii  libvdpau1                                         0.7-2                     
         amd64
ii  libxine1                                          1.1.21-2                  
         amd64
ii  libxine2                                          1.2.5-1                   
         amd64
ii  nvidia-vdpau-driver                               331.67-1                  
         amd64
Currently I had the desktop effects disabled in KDE.


With the package from Wheezy this issue is not visible.
http://ftp.de.debian.org/debian/pool/main/k/kaffeine/kaffeine_1.2.2-2_amd64.deb


With version 1.2.2-3 kaffeine is starting to link against libxine2 instead of 
libxine.
http://metadata.ftp-master.debian.org/changelogs//main/k/kaffeine/kaffeine_1.2.2-3_changelog


libxine2 supports the video output driver vo_vdpau which is in use when the 
problem is visible.
(Due to output when starting from command line.)


When forcing in ~/.kde/share/apps/kaffeine/xine-config the use of another
video out driver I could also not see the issue anymore.
-#video.driver:auto
+video.driver:xv


But I suspect that these two workarounds would lead to loosing the
hardware acceleration, which vdpau would provide.


When the problem is visible, viewing something in windowed kaffeine and 
changing to another
application leads most of the time to the whole picture gets black - sound is 
playing.

When opening a menu from the menu bar and iterating through the items there 
most of the time
the rectangle of the before visible menu stays black while the video plays just 
fine in the
area which was never hidden behind a menu.


The third workaround works in my case also with 1.2.2-3 and automatic use of 
vdpau by just
activating desktop effects in KDE by hitting alt+shift+F12.


@Alex: probably you can check if my findings apply to your situation too.


Kind regards,
Bernhard

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