in both official blender builds r46461 and r50064, I get the following problem with the attached simple test file.
I generated a cycles material that does not cast a shadow. This works (ie. there are no shadows from that material) if I render with CPU, but there are shadows (ie it doesn't work) when I render using CUDA.
Please let me know if you need more information about my system. FYI, I asked a few guys on IRC to test the file, and they had the same issues.
please always mention your computer specifications!
I can't confirm the issue here (Windows 7, nvidia 540) and SVN 50079, most likely you have a old gpu with computing capability < 2.0 and therefore no transparent shadows. That is a hardware limitation and not a bug.
Sorry for not mentioning the computer specifications earlier.
The system is a 64bit Linux Mint 13 with
NVIDIA Corporation GT200 [GeForce GTX 260] (rev a1)
Apparently, this card is capable of cuda compute capability 1.3. I don't know in detail what that means, but it's probably the hardware limitation Thomas Dinges mentioned.
Sorry for the false bug and thanks for looking into this anyway.