I have experienced similar - All using x1.0-rc3 of Sikuli.

Since I use this for work I've been investigating the extent of the
issue.

Host Win7 and guest Ubuntu 12.04, VMWare Player and Virtual Box default setting 
- screen goes black on capture.
Host Win7 and guest Ubuntu 12.04, VMWare Player w/ 3d acceleration - screen 
goes black on capture but text area of xterms is visible with masking by any 
other windows (eg Firefox)
Host Win7 and guest KUbuntu 12.04, VMWare Player and Virtual Box default 
setting - screen normal on capture - SUCCESS.
Host Ubuntu 12.04 and guest Win7, Virtual Box default setting -  screen normal 
on capture - SUCCESS.
Host  Ubuntu 12.04 and guest Ubuntu 12.04, Virtual Box default setting -  
screen goes black on capture.

I suspect the slight variation when 3d acceleration support is enabled
leads me to think the screen going black is the interaction between
Sikuli screen capture, a specific style of compositing window manager
and para-virtualization of the graphics hardware - so Sikuli is unable
to access or accesses the incorrect frame buffer for capture.

-- 
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Drivers, which is subscribed to Sikuli.
https://bugs.launchpad.net/bugs/752065

Title:
  Screen goes black when capturing image when running on VM Fusion

Status in Sikuli:
  New

Bug description:
  Screen goes black when capturing image when running on VM Fusion.  Guest OS 
is 10.6.2 Mac Server.  Host is 10.6.6.
  Version X-1.0rc2

  Repro Steps:
  1.  Launch Sikuli IDE
  2.  Click on the Take Screenshot icon
  Result --> Screen goes black and I can't see what it is I want to capture
  To get screen to back to normal, I have to drag mouse to capture an image (at 
some random rectangle on the screen).

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