After updating to QuickBooks 2014 R3, direct deposit paychecks display with a negative value in the bank reconciliation screen. This does not affect the actual bank balance in the bank account.
This issue has been resolved in the latest release for QuickBooks 2014
Update to the latest release:
Go to the Update to the Latest Release web page.
IMPORTANT: Make sure your product is selected. If not, click the Change link and select your QuickBooks product.
Select and follow the instructions for one of the update options: