I think I've finally fixed this myself. I was about to jump through some pretty serious hoops, then thought about a "move and nuke" approach. When getting ready for this I looked carefully at the email account creation prefs in the DreamHost panel and noticed an auto-archiving setting.

Immediately I switched over to the accounts I've been seeing the mystery folders on and sure enough, they had this enabled with folders named "Older" - Arrrrgh! I thought that I'd created those "Older" folders originally on the client side so it never occurred to me that there was a process on the server that I could control for this.

I've just set them up in the server-side prefs to use the folders "Archive" which should now solve the issue.