Files downloaded recently are all correctly marked and files marked to be hidden are also correctly marked. All files older than the download limit for new groups are marked "old posts'. Does this fit with the corrupt db theory?
I don't really know why you're seeing "Downloaded" go away. If the files that are tagged "Downloaded" are only the ones you just downloaded in this session (without restart) then it's probably a corrupt DB and you'll need to delete "DownloadMarker.db3". If you have some marked downloaded across sessions and some not then it makes me wonder if the DB file had gotten deleted at some point and was just now building itself back up.