I have managed to fix this for anyone who's interested. The problem was caused by the certificate template I used when I created from my CA server. It should be a web server certificate template and I left this setting at the default which is set to Administrator template.
To recover the appliance this is what I did:
I downloaded a trial version of ACS 4.1 for windows and installed it onto a Win2003 server.
From the console CLI connection on the ACS appliance I did a backup of the device and put this onto my FTP server.
Then I restored this backup to the Windows ACS trial version. I immediately had the same issue with unable to access the GUI due to the certificate issue.
I then went into the Certificate Snap in via MMC and found the certificate and CA certificate and deleted them and rebooted the server. Now I could access the GUI correctly and the management access over HTTPS was now turned off.
So then I created a new certificate from my CA server, with the correct template and installed it onto the Windows ACS server. I tried Management access over HTTPS and all good but decided to disable this as not required. (The certificate is for PEAP authentication). Then I backed up the Windows ACS and restored it into the appliance - hey presto it's back.
Moral of the story - don't use Management over HTTPS!!