I think that might have been because you completed an IR prof check. Do you hold a current IMC or IR on your JAA licence? If so no need to do the IR profile just do the IMC prof check and apply for your PART-FCL licence with an IR(R). An EASA licence cannot contain any non-EASA ratings therefore you couldn't have an IR and IR(R) as they are technically the same thing although this is just my opinion not fact.
Let me know what the CAA say.