Tried doing that.
Any new site I made had all co-domains put on that one site... so what I did was to delete the site that seemed to have gained superpowers (own all co-domains).
When I did that a new entry showed up in DNS view of ISPconfig2.
I clicked the site but it showed up as a normal site config docid which was odd. Deleted that one as well.
That seems to have fixed it.