It happens when trying to visualize a RGBA image as a 3D model.
As the volume rendering is turned "on", it automatically select the "GPU Slicing" method, that does the correct job, as shown in picture "mitk-bug-transparency-1.png".
However, if another method is selected, the render will not be correct (or am I mistaken ?).
GPU Raycast & GPU MIP Raycast will produce a 3D render of the single selected slice (mitk-bug-transparency-3-VR-GPU.png).
If the setting is set back to "GPU Slicing", it'll create a "black fog" completely opaque similar to "CPU Raycast" output.
CPU Raycast will directly produce a "black fog" (mitk-bug-transparency-2-VR-CPU.png).
CPU MIP Raycast is the same as CPU Raycast, but with some gray features displayed (mitk-bug-transparency-2-VR-CPU-MIP.png).
At the moment it was only tested on Windows with MITK 2013.03.