Hey Hugo thanks for the reply, I appreciate it. You are correct, it is a custom theme and I am almost 100% certain the custom theme is having a conflict with BuddyPress. The site is a live site so I would rather not switch the theme, but I am sure switching to twentytwelve would solve the problem.
I wasn’t sure if duplicated content was a known issue when using custom themes or if anyone had experienced a similar problem. I wasn’t sure if there was an easy code fix or not.