Nah. You can tell when it was quoted with the quote feature because it actually links back to the quoted post. I doubt anyone would do that manually.
I actually did it manually once when cross-posting from another thread, not to mention a few times before that, before I understood how to use the multi-quote function. Although, that said, I do agree that I very much doubt that's the cause of it, or at least the sole cause, since I'm sure it's incredibly rare for anyone to do so.
As long as I'm posting, I suppose I'll add my voice to those who've already said they experience this problem. It almost seems a shame that it's not more common than it is. As it stands, for me at least, it happens so infrequently that it becomes basically impossible for me to get any sense of what conditions might be causing it.