rsync not deleting files

I’ve been using rsync for years to backup to an external disk, currently version 3.1.1 in OSX 10.9.5. Some time in the past year rsync stopped deleting nonexistent files, but only in some folders. For example, in my external disk’s ~/Movies/ folder I see files and folders I deleted months ago that are still there. Meanwhile in the Desktop folder files get deleted normally. This is happening on my two backup Firewire disks so it is not peculiar to the disk.

The only thing I could think of is that permissions on the Movies folder look like drwxr-x—@ while on the Desktop they look like drwxr-x——. So I thought it was corrupted ACLs, so I booted into Recovery and ran resetpassword and reset permissions on my userfolder but it didn’t help. I searched the internet thinking maybe it was a known breakage but found no such clues. http://rsync.samba.org/ shows no broken OSX syncing, and a bugfix list for a candidate verson doesn’t mention anything.

I do have verbose setting so I see what is being deleted, but rsync doesn’t even see files missing on the source that exist on the destination. There are no error messages pertaining to those files. The command I use looks like this:

rsync -aAEHSWX --progress --delete-excluded --exclude-from=/Volumes/$USER/.rsyncBackup /Volumes/$USER/ /Volumes/Backup/

I even added --delete-excluded in case something in my exclusion file was matching some files.

Does anyone know what’s wrong?