This is not a problem for me on mac using Preview (ignore the window drop shadow in the middle):

- Alchemy | Preview.app (Mac OS X)
- Transparency.png (32.07 KB) Viewed 528 times
But I can imagine your Pdf software is converting RGB > CMYK - which would give you slipping colours.
I'll have a look into a work around.
In the meantime I would be interested to hear what software people are using and if it displays the colours correctly or not?