I tested it in latest Stable A3 release 0.60 and error still occurs. I tried different input images (PNG 32bit w/ Alpha mask, TGA with Alpha mask layer) converted in Bohemias TexView2 to *.paa files. Colourful images in Texview2 work, base image and alpha mask are shown properly. When in game they become single colour (grey), semi-transparent images.
Would be nice to hear if there is solution for that issue. It may hold many mod developers.