Folders should be included in the .XnViewSort file, if I manually edited the .XnViewSort by adding folder names in the order list, save the .XnViewSort and F5 refresh in XnViewMP browser, the Folders order did get custom sorted, but if any sort order changes is made in the browser, when .XnViewSort is updated by XnView, the manually added folder names entries are lost of course.
edited .XnViewSort example
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XnView sort
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Folder_A
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Folder_B
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Hope you can implement this custom sorting for folders. Thanks.