Attachments Not Being Deleted When Messages Are; Preference Set Correctly

I have multiple copies of attachments remaining on my hard drive after the associated messages have been deleted. These are almost all PDF files (which I know I haven't edited). My preference for this has always been set to "remove unedited downloads after message is deleted." Right now my workaround is to export the mailbox, then reimport it, which then cleans out the unassociated attachments.
Anyone else experienced this? I guess maybe I should try trashing the Mail preferences file to see if it's been corrupted somehow. Which one would that be? Any other suggestions?

I have done some more research and can clarify the problem. I use an IMAP account, but I save messages to folders on my hard drive. So right now in a certain local mailbox folder, the messages in my subfolder are numbered 118XXX.emlx, but I have a bunch of folders in my "attachments" folder numbered 107XXX (this is after a rebuild). For example, right now I have three copies of an attachment in the local mailbox folder and one in the "Mail Downloads" folder.
So this is the proximate cause. When I delete message 118904, then it will remove the attachment folder 118904, but the others remain. So then I have attachments without the messages. Similarly, when I archive the mailbox, only the existing messages pull their attachments to the archive, so the archived mailbox is repaired.
Now for the root cause (I think). In order to sync between home and work, I dump (just) my "Library/Mail/Mailboxes" folder on a USB stick and then take it to the other machine. (Yes, I know this is a bassackwards way of doing exactly what IMAP is supposed to do, but I am uncomfortable with having my messages on our work server, both for privacy reasons and because the server is notoriously flaky.)
So I'm guessing that in the context of just transferring this folder (in contrast to pickup some of the .plist files too), the tables of contents are getting messed up. I would prefer not to move the whole "Library/Mail" folder, because there is still quite a bit of stuff stored in the IMAC-associated folder. I could also just do an archive every night from Mail instead of a copy in the Finder (I did the latter because it was easy to automate).
Any other suggestions? Should I just copy the .plist along with the Mailboxes?

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