I think it's only happening for threads in User Uploads. The problem is the ":80" in the URL, it specifies that the traffic should go over port 80. Now port 80 is only used for HTTP traffic, which is why those links still work, but HTTPS is typically received over port 443, so they don't work. Leave out the number altogether and the browser will use the correct defaults automatically.
Are you using Chrome? If so, try allowing the 'unsafe' components to be active, the button is at the end of the address bar. I tried this, the [youtube] embed worked again (it didn't work before) and there is no more :08 in the url of the link to my posts.