It may be possible that when you add the word to the dictionary in Sigil that the defaults file is not immediately updated - it might only write it on exit. This is unlikely as I think we flush it to disk, but its why I wanted you to exit Sigil before checking the file.
But in any case, this is definitely odd. No one else seems to be having the issue (although it has been pretty quiet around here) and I think I've run out of questions for the moment.
So you add the word in preferences, close the dialog, then open it again and the word is not there. But if you look in the default file the word is there. Hmmm...
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