I managed to resolve this myself by generating a certificate in the swtich software and then download it before comparing it to the certificate I generated using the EBJCA software in our lab. It turnes out the switch firmware doesn't like the following extensions:
X509v3 Key Usage: critical
Digital Signature, Key Encipherment
X509v3 Extended Key Usage:
TLS Web Server Authentication
X509v3 Subject Alternative Name:
To resolve I exluded the above and generated newone and hey presto it worked.