Just determined that it's some issue with inputting TIFF images. When I convert the input images (1.tif 2.tif 3.tif ... etc) into PNG using imagemagick's convert and then run enblend 4.1 on them, it comes out fine. The input TIFF images are from nona, so I tried opening in gimp and resaving, but still the same issue - the output is washed out. Convert to PNG and use the PNG files as input but output a TIFF file, works fine too.
Looks like it's something with the reading in and decoding the image that's causing the problems, because outputting a TIFF image isn't a problem. It's only when TIFF is being inputted.