So, i have a domain hosted with my provider, lets call it mydomain.com, everything runs fine.

I want sub.mydomain.com to point to my own server at home, so from what i gather this is what i need to do:

Login to mydomain.com and add 2 dns ns records as follows:

sub.mydomain.com. 600 IN ns1.dynu.com.
sub.mydomain.com. 600 IN ns2.dynu.com.

That's all i need to do on my hosted domain and this should now be ready to run through dynu correct?

So all i need to do now is go to dynu.com, create my dyndns service pointed to my own domain sub.mydomain.com and voila it should work right? Yeah well it doesn't and i appear to be missing something, any help?

I have ddclient set up and working, i can access my home server from its ip but not sub.domain.com so that's not the issue. If i set up a whatever.dynu address i can of course access my home server, if i then addd a cname redirect it works, but for security and ssl etc i don't want it running that way, so yeah any help?

Check the name server records for sub.mydomain.com using this propagation tool. I feel that the name server records have not been set up correctly.

It seems you are right, deleting the dynu hosted domain results in no ips, re adding the chance to my host and dynu domain results in ips which point to my server, am I to assume that the issue is then with my host? It seems that although I have added the ns records it is not using them

You will need to check with your host for that. Most DNS providers do not allow you to use a separate NS server for a subdomain.