I would say most of the time it does not say that 100% of it is there even though it is the same file I had downloaded from that site.
Basically I downloaded this original file and then I seeded it for a while. I removed the torrent from the seed box as well as the file. I re-upload the exact file a bit later for a reseed and upon a force recheck it always says 99.9%. Somehow a few KB to 1MB just disappeared out of nowhere.