I'm afraid I can't help you with a hard and fast solution. Instead, I would like to add to the discussion the experiences I've been having with JS export from Flash CC2015.
I made sure the PNGs that went into Flash were sRGB for best colour compatibility between browsers. I made sure to specify in the image property in Flash to use the original image upon export. Result: Flash changed the colour space of the images when exporting.
Now I deal with an agency that does not want images in subfolders. But Flash does not allow not specifying a subfolder. So I export once, drag the images out of the "images" (default name) folder and erase the directory in the JS manually. Result: The images show in the animation, but at a different scale and different placement (with a different anchor).
Apparently the only remedy to all of these issues is: Turn off image export in Flash and MANUALLY paste the original images (pre-Flash) into your output folder. Every. Single. Time.