Not sure how many people experience the same issue, but here is what I tried.
I had 1 top-level folder (Video) plus $RECYCLE.BIN and System Volume Information. Within the Video, I had 2 folders - Cartoons (25 files, 66Gb) and Movies (49 files, 200Gb). Total volume of data is not excessive, as you see.
On the initial scan (when the router is rebooted, or when the storage is ejected and then connected again), only a handful of files were visible in the Cartoons folder, but the Movies was not visible at all.
When I move (drag and drop) the invisible files from the Cartoons folder into its parent folder (Videos), they become visible to the media player. I tried in groups of 6 without any problem, but when I moved a larger group of files, occassionally the media database of the router becomes corrupted and the media player shows that there is no media in the folder (and all folders become inaccessible). When I moved those files in small groups back to the Cartoons folder, they stayed visible, but again, when I tried moving a larger group (20+), the media database becomes corrupted, and the drives has to be ejected. What it interesting, is that when I move the files up to the parent folder, the storage drive indicates activity similar to scanning, but then I move the files down (to the nested folder), the storage drive shows no activity.
My next test was moving all cartoons to the root folder. Same results - only the first 6 files are visible to the media player, and moving larger groups crashes the media database.
I have now two theories of what is going on.
1) It looks like the router's interface with the attached storage is just too slow, and any fast or sizeable change on the drive crashes the router's media database.
2) It is also possible that on scanning the storage, the router doesn't wait long enough (as in the case where only 6 of the 25 files in the root folder are visible).