The default JPEG format of the thumbnails cannot handle transparency, so for the moment, only the background color of the transparent png/gif is filled with the selected color (by the parameter
bgcolor=#ffffff). It is quite difficult to create a transparent thumbnail with PHP-GD only (to code it; for some php-installations it is impossible; also more memory is eaten).
On the other hand, it is trivial to produce a transparent PNG with ImageMagick, so I am considering adding such a feature. If you have ideas of the implementation, let me know.
The first suite is with added bgcolor=#ffffcc, and it is set as background in the images too: that's why they seem transparent (although the thumbs are non-transparent JPEGs). The second suite uses the same files, with the default (white, #ffffff) background color.