I use a soft lens brush on my slides before scanning, and usually a few black spots persist. Most times, I believe that they are dust particles that are more firmly stuck to the film, but I have also heard of cases where Kodachromes have developed a "mold" in the emulsion. I have seen a very few of my slides that may be exhibiting this issue, and that's the reason that I have begun a very long-term project to digitize my entire collection.
No matter what the cause, I clone out the remaining spots while processing in Lightroom.
Doug Lilly
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