I have noticed that some stockpiles in my base are missing the "allow rotten" or both "allow rotten" and "allow fresh" checkboxes. (I have verified that copying settings from other stockpiles does allow me to change them, though.)
I believe this could be a one-time issue related to updating from 1.0.2055 to 1.0.2057, as it happened shortly afterwards, and new stockpiles I create seem to always be correct. I couldn't find a release announcement board or I would have posted there instead of here.
(I have screenshots but they are too large to attach, and they don't contain any more information than I gave above.)
I believe this could be a one-time issue related to updating from 1.0.2055 to 1.0.2057, as it happened shortly afterwards, and new stockpiles I create seem to always be correct. I couldn't find a release announcement board or I would have posted there instead of here.
(I have screenshots but they are too large to attach, and they don't contain any more information than I gave above.)