So this is new.

I uploaded a torrent with QTM, redownloaded the *.torrent file as usual, loaded it into my torrent software and after hash checking the torrent it only got up to 98.5%, as if somehow there is 1.5% of the data missing in my own files. I haven't deleted any files from the folder - it's still identical to what I originally put in the torrent, so I'm totally baffled.

If you are 100% sure that you didn't change the name or make any alterations, you could have had a random data loss from corruption of the drive.  Every few months I verify the data for all of the files I'm seeding and sometimes one or two are missing small amounts.  I think sometimes it may be caused by moving the file and it can definitely be caused by deleting some of the files in a multi-file torrent.