There is a known issue with the EE_Cert patch from the gateway that when not installed first, it can fail to apply properly and will throw this error I believe.
As far as I am aware, the workaround is to reset to factory, then install the patches again making sure you install the EE_Cert patch first.
There may be a way to just re-apply this patch, but you may need to open a ticket with support and see if they have a way to do this.
I just ran into the same issue. Is there a way to get this CC_cert patch reapplied so that I can create a CSR?