When the report calculates the various sections it only looks at the posted gifts for the revenue. It removes the pledge payments from the posted gifts. Thus the pledges are not included from the pledge posting nor from the pledge payments. The only way to manage the reconciliation properly is to use a different account for pledge revenue.
If you have already set up the accounts, then you will need to add a new account to the Master Chart to represent the pledge income, build the account for the funds, add the appropriate account in the fund class defaults and then make journal entries to reclass the posted pledge revenue from the gift income account to the new pledge account.