Your comments

I've tried combining all 4 files into one
priv.key
domain.crt
intermediate.pem
root.pem

but alas, no luck, I'll go and post on startssl and see if they've got a tool for combining it, is it possible the ssl engine in python can't handle it for some reason?

The `no shared cipher` bit is strange.

If I get ajenti running with the generated unsigned cert can I configure nginx from within it to host it? Sounds a bit dodgy
https://www.ssllabs.com/ssltest/analyze.html?d=prowl.autonomicpilot.co.uk is the same cert but on a different server and not combined into a single cert
yes, it's just when trying to combine the custom cert into a pem for ajenti, openssl validates it on the command line `openssl x509 -in certname.pem -inform pem -noout -text`
Sorry I realised I'd pasted the wrong error message, have fixed it now