Interesting, I've never had this problem and have been using the auto upload for many years. I only use it for the photo taking, though. Any time I go through a phone cleanup and delete photos and videos, I'll look at the folders I backup to on nc and actually go through them carefully to make sure everything was uploaded.
My install comes from f-droid so not sure if that's something to do with it (unless yours is too).
I'll be honest, I think the grammar and way the post was written is what's annoying me most. I'm reading it with at least 3 different possible meanings.