As of Version 4.8 of QuoteWerks, the main executable of QuoteWerks has been code-signed. This some times causes Quickbooks to not recognize the integration after certain upgrade points. Thus your Quickbooks Integrated Applications may be seeing it as different. To fix this, you will need to rebuild the integration.
Get everyone out of Quickbooks. Log into Quickbooks as THE "Admin". Then switch it to single-user mode. Then go to Edit -> Preferences, click on Integrated Applications, and then click Company Preferences. Select QuoteWerks and remove it. Then bring up QuoteWerks, click the Quickbooks button, then click the Setup button. Quickbooks will pop-up with it's integration wizard. Select the option concerning having Quickbooks open, then click through the wizard to finish it.