Hi, this is a commons issue, I was also facing.
So far what I know, Pipedrive evaluates same threads based on the same subject and two same emails in the email. This is in order to prevent threads from matching. However, when someone sends multiple emails with same subject and you are for example with someone in the cc, then it is a problem. We are just trying to avoid it by using different subjects every time. But it is painful and would be nice to change it.