If you're not getting response here, it may be because not many people have used the Kindle plug-in. I've not tried it. The plug-in usually lags the InDesign versions. I think the current version recently added support for InDesign CS6. EPUB guru Anne-Marie Concepcion twittered this week that she thought the plug-in was much improved but still recommended using the EPUB to KindleGen method.
You might also try posting on the eBook forums like this one:
Thanks for your reply.
I forgot to mention in this last post that I'm using InDesign 5.5 on vista. I used the InDesign "Export for Kindle" version 0.971.
The epub to KindlGen method creates causes a loss of image transparency.
It may just be a Kindle limitation. Check out the link I gave you and look for Kindle forums.