I would guess that when you completed the Tax Return for 2014, you only declared the loss and made no reference to the fact that you suffered PSWT during that year.
Even where it is repaid to you during the year by Revenue, you still need to state the tax on the Return.
Before you send in a claim for an interim refund of PSWT, your account with Revenue is basically Nil. When you receive the interim refund your account is then in a minus balance for the amount repaid to you. To balance this out you need to declare on the Tax Return the total PSWT figure - it's on the same section of the Return as where you declare your self-employed income.
If so, ring/write to Revenue and ask them to check what amount of PSWT/F45 certs they hold on file for you for 2014.
They should then amend the assessment to include the PSWT which would correct the imbalance.