So it looks like the stores certificate is still not working. As you can imagine it doesn't help generate customers when customers see a big sign from their browser saying "THIEF" every time they try to go to checkout!
I'm looking into this again and will hopefully get it fixed. The problem is basically caused because my domain name (the panzer-command.co.uk) is held by one company and the website and store by another so I have to redirect from the UK company to weebly. For some reason the SSL (the security part) doesn't like this at the moment.
You can essentially skip the warning without any problem. Payment on the site is handled by Paypal so when you go to make payment you will be redirected to their payment portal and therefore their security.