Okay, was just informing you that the error persists for our community, and that not everyone gets the error, just a substantial number - an issue that started to occur with the last update.
The issue doesn't occur with .PBOs, only .bisign files. It is not a partial file transfer issue for us, as doing what you mention to the .bisign files is perfectly fine - they update no problem. The fix is to delete them, to which sync will then download the file just fine.
I will run ArmA3-Sync Debug by default now, so if the issue does happen again, I can screen shot it for you.
Edit: Just found out, the guys who don't have the issue are the ones on 1.6.92, and the ones with are 1.6.97.