BRU application does not load the Filters (12) > Subfolders setting saved in the .bru file (aka, your saved favorites file) when ran from the context menu. The .bru file does properly save the setting on line 77 as below, and when opening the .bru file directly from within the application it enable the Subfolder option if saved, but when opening BRU application from the context menu it fails to load the setting at all.
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Subfolders=1
(also, hiding the Sub. Directory column keeps re-appearing even though it was turned off)