Might be due to file types in your different folders.
Try this: take one of your files known to work with the BD-390, make four copies of it with slightly different file names, move them to the other folders (one per folder), and check if the BD-390 can read them.
If it can, then your problem may be caused by limitations on file format compatibility of the BD-390, in which case there's little you can do but hope LG issues new firmware supporting more formats.