I'm currently following a rendering problem of a poster. While doing so I found a first lead, that resulted in a first patch.
The PDF I'll attach contains an image with a mask applied to it. If rendering works correctly, only a single green "OK" should be visible. With pdfbox 2.0.3 and HEAD I get a white sheet.
I tracked this down into SoftMask.java. There a source raster is sampled by querying the pixel data via getPixel(int,int,int). This will only work correctly for RGBA input sources. In my case the input image is an RGB image and getPixel does not overwrite the initial 0 value in the rgba value array.
The attached patch uses the colormodel corresponding to the source raster to convert into the components. This correctly returns the alpha value of an RGB image as 255.