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@jesscat - I don't know what's going on for you. I don't get that behavior.
I have a boolean custom column, with tri-state bools enabled in Calibre settings, set from bookmarked very similarly. My custom column is left 'null' when none of the stories are bookmarked, when one is bookmarked, or when all are bookmarked.
I put in some debug output and the values are exactly what I expect and behave as predicted.
The only thing I can think of is if you have replace_metadata settings that remove 'False' values and there is exactly one bookmarked=='True' story in the series. Except that you said you don't have any other bookmarked references. (Or, I suppose if you're setting it from the Custom Columns tab by mistake.)
If you look on the personal.ini tab, there's a 'View "Safe" personal.ini' button. I might be able to help more if I see your entire personal.ini. [CODE] tag is helpful for that, or attached .txt file.
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