You mentioned some temp file appearing and disappearing.
If you enable 'show hidden files' and uncheck 'hide protected system files', and keep a sharp eye on the folder when you use your shortcut key, maybe that gives some clue about what's happening?
Are there any files in these folders that get their timestamp changed?
(e.g. maybe a hidden folder.jpg)
Very good suggestion: I've determined that the creation of a Thumbs.db file is what's causing the folders' date modified attribute to update. As for why some folders have a Thumbs.db and some don't, I haven't the faintest clue. I could have sworn Windows just made them automatically. As for my initial sighting of a temp file being created and removed, that wasn't the Thumbs.db itself. No idea what that could have been.
Looks like instead of just making one whenever the folder is accessed, and since I don't actually access the folder after putting it in my library, it never got a chance to create one?