Payment Journal not reflecting payment made that is shown in GL

I found one of my monthly payments not recorded in the payment journal for the CRA yet it was in the GL for the month .  The month was reconcilied and CRA payment made but working with the T4 Summary showed the error.  I recorded the payment with the date it was made Juy12 for the month it was due June remittance on December 31. This is showing up once again in my Bank Reconciliation as outstanding. As well, now my GL for the month of June is showing two payments made to CRA. 

Please tell me why this has happened and what I can do to correct. 

Thanks.

Jeanne