As reported on the CHDK Facebook page, there are issues with images taken with the DNG version set to 1.3, instead of 1.1. Images have darker, coloured spots on them, which are particularly visible in lighter portions of the image. It is unclear whether these spots result from a bug in CHDK, or one in DCRAW (and by extension, UFRAW, and other programs that use DCRAW as a basis for conversion). These are not bad pixels, which by definition are lighter spots more visible in darker regions of an image.
I have discovered the following workaround:
1) Use the free Adobe DNG Converter to convert your DNG files to new ones in a separate subfolder.
2) Open these files with Irfanview and convert them to a regular graphics format.
Before image (excerpt, with spots):
After image (same excerpt after conversion with Adobe and view in Irfanview):
Hope this saves someone from too much grief.