So I fixed the problem and it was incredibly simple.
I had my URL redirected to www.mywebname/zencart and it was a "frame" redirect so the user would just see www.mywebname.com in the address bar.
I changed it to a standard redirect so the address bar shows the actual address i.e. www.mywebname.com/zencart as the start page and everything works perfect now.

Hope this helps anyone else with a similar problem.