Are you using QuickBooks and also TurboTax Business (the latter to prepare your 1120-S)?
Reconciliation discrepancies are not something that would be entered as income or expense items unless and until you are aware of the actual source. Most likely, you have an unrecorded check or deposit, a duplicate payment, et al, that you need to track down.
You can use returns and allowances or other income for refunds (in the Income section) and rents (in the Deductions section) for the rent the corporation paid.
