If you did submit in Dec 2012, then your Eligibility should have been done by CIO. From what I understand about post July 2012 applications, Officers at CIO open the documents, Check for document completeness, perform Eligibility test and create a file in GCMS. After that, they issue you the medical and start your criminality check. Then, they forward the application to CPP-O for further processing.
Sincerely, I don't understand why they waited till June 2013 to do your Eligibility. It may be that the Officers at CIO did not do the Eligibility check.
By the way, when did your application go 'in process'...Applications go 'in process' only when Eligibility is passed. On another note, your Eligibility may have been passed a while ago & it is not updated until June 2013 when an officer looks at your file. This happened to me in the case of my criminality...It was passed but refused to be updated for sometime.
Hope this helps!