Something is definitely not right. I'm suspecting the DNG conversion may have something to do with it. What do you use to convert to DNG? The RAW converter that opens up the RAW file (such as Adobe Camera Raw - stay far away from it for AP-related use!) before you save it again may be applying all sorts of operations that could be causing your issues such as color balancing, noise reduction, sharpening, etc. because it assumes you want all that done as it assumes it's your one and only image (and not just one out of several to be stacked and processed linearly).
If your camera is not supported by DSS directly, I would recommend seeing if it is supported by the latest dcraw command-line utility for your operating system (which many RAW converters use internally).
Using that you can convert the RAW files to something that'll work even better with StarTools than what DSS produces (see here).
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