This problem, first reported in September 2016 still exists in the latest portable version (5.00.2581). I am still using Win 7 x64.
The problem in summary is that only some nested folders are shown as subfolders of a favorite listary folder when the favorite listed folder is automatically expanded. A full report with screen prints is shown under the similar heading (Favorite subfolders not listing correctly in Portable v5 (Win 7)) In Sep '16.
Because this is my main use of Listary (to quickly specify deeply nested folders when saving or accessing files) I have again reverted to version 4.23.1728 which works perfectly.