Different sites accessed by LeechFTP and DH FTP

I have NO IDEA what the heck is going on. I created a folder in one of my sites through Cyberduck (Mac) at work the other day, dropped a couple of files in it, and off I went. The site seemed “empty,” but I didn’t worry about it too much at the time. I haven’t used Cyberduck much, and thought I just had something configured wrong to view the folders correctly.

Yesterday, I used LeechFTP to log in and transfer some files, and got the OLD file structure… not visible from Cyberduck. And the new folders (added through Cyberduck) weren’t there. So I uploaded a file into a folder in the OLD file structure. But I can’t see the old file structure through the DH control panel, or from Cyberduck. I can only see the new folders.

I seem to have two parallel sites: one “real” site (the one I can upload to, and retrieve from, and view from the DH control panel) and one “phantom” site (accessible only through LeechFTP.)

Can anyone help me figure this out? I’d like to reconcile this, especially since the file I uploaded through Leech is f?%$in’ huge and I don’t want to go through the two-hour wait to re-upload it again.