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7020100
(Get the code!)
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.