InDesign CS5.5 will by default save images with the Automatic setting, which I think creates JPEG files usually. These would not support transparency.
Have you tried saving the EPUB files as PNG files. These support transparency.
Then the question would be: Does your converter software and MOBI support the PNG format?
(I see your question also posted in the MobileRead forum. The suggestion was to make a screen capture, but I don't think that would include transparency.)
Can't say I've tried it but if you can't get the PNGs to make it through with the background you could always try replacing them in the EPUB after export.
I imported all of the images as TIFF & specified PNG in the export options.
For EPUB to MOBI conversion I am using Calibre.
What next I'm not sure - I am loathe to put out a book that doesn't display properly in Kindle's rather nice Sepia page colors!
Yes, I guess so but I want to retain the automatic device related image sizing features that inDesign now supports.