Maybe try uninstalling it? Do you have the trainer installed? I'm having kinda the same issue and I would like to have help too.
I have installed a handling.meta for Sideways Inc. server and when I'm playing on other servers, the red square appears. Now, I know you might say that the Handling can be the issue, but I tried today earlier 2-3 times in a course of few hours and It worked, I had no red square. But now, it's little past 8pm and I'm having the red square again.
I think it's either the handling, or my internet connection, but I would like to hear other opinions.
EDIT: Tried installing the handling.meta. Didn't work.
EDIT 2: Tried with a friend of mine. He also got read square, but we can talk in the chat. Just can't see each other