I just posted about this same issue on another thread: "GST/HST Installments and Annual Returns"Hope that helps resolve this, although this is an old thread.
Also, regarding the journal entry to reflect the refund you have received from the CRA, I believe you may have done that backwards.Credit the bank account (CR r...
I faced a similar problem, with the Q4 instalment not contributing towards line 110 of the HST Return, since the return is dated for the fiscal year end. I had ...