This is not a limitation of our sync utility… it is a limitation within QuickBooks itself. You can get more information about this limitation from this Intuit Knowledgebase article.
When utilizing the Seamless sync, a connection is established for up to 3 minutes each time you add/edit/sync any information to QuickBooks. So if you wish to use the Seamless QuickBooks sync, but you also need to close your QuickBooks file, you will be able to close the connection 3 minutes after your last synchronization task has completed. You can check whether or not the connection has closed by observing the ‘QuickBooks Status’ label on the far-right part of the toolbar on the Contacts tab. If the text is in green, the connection is open. If the text is grey (or not visible at all), then the connection is closed and it should be safe to close QuickBooks.
If you require to close the QuickBooks software frequently, you will not be able to utilize the Seamless features of the sync. You can disable the sync by unchecking the ‘Update QuickBooks when adding/editing contact information’ option under the ‘QuickBooks’ tab of the ‘Integration Options’ form accessed from the Menu at (Setup -> My Company -> Information & Settings -> Integrations).
If you disable the Seamless integration, you will need to manually synchronize all information using the menu items under (Setup -> QuickBooks) or (Contacts -> Import/Export -> QuickBooks).