Run the P&L by customer in QuickBooks. ConnectBooks imports each store's data into a separate customer, so you can compare 1 store at a time to find the issue.

Check that all settlements are in QuickBooks. Make sure all settlements for the period are exported to QuickBooks, including settlements that span 2 months. For example, if you're checking January, make sure a settlement from January 28 to February 10 is exported. Settlements that are still open are hidden by default. To see them, turn on Show Open Settlements on the Accounting Export page.

Check report settings in ConnectBooks. Click Customize and set Transaction Date to Posted Date, since QuickBooks uses the posted date.

Check for open balances. Look for any open balance on the store's customer in QuickBooks. The balance should always be 0. If there is one, clear it or contact ConnectBooks support.

Make sure no settlements were deleted by hand in QuickBooks. Check that all payments are reconciled.

Make sure the settlement with the monthly storage fee is exported to QuickBooks. This fee is usually billed the next month and dated back to the month before, in QuickBooks and on the P&L report (unless your account settings say otherwise). If that settlement isn't exported yet, the fee shows in your ConnectBooks P&L but not in QuickBooks, so the 2 reports show different totals.

Check for fees you uploaded by hand. Fees you upload in ConnectBooks show in the ConnectBooks P&L but aren't exported to QuickBooks, so the 2 will differ.