Transparent images lose their transparent pixels when displayed in CQ. You use /apps/Components/image component to display your images.
Flatten the layer with a color that is not already in your image (for example, cyan). Then, set the transparency to the same color in /apps/Components/image/ImageObj.esp writeLayer()
The transparency in GIFs is done marking one palette index as transparent. When flattening the layer, the previous transparent pixels could get another color.