Yes, it is a known issue.
The problem is fixed in CS2 (well, mostly fixed)
Grayscale images with transparency will inverse their colors when saved to pdf. You can to 1.3 compatible pdf and the image will not invert.
There are a few ways to go about this, but my memory is faded on the issue to recall the other methods of preventing inversion. You will need to find the best workflow for your needs.