Your first step would have been to set up the "link" to your company file. When you did menu Tools->QuickBooks Billing/Customer Update->Set Preferences and clicked the "Browse" button and chose your company file, did you, at that time, not received the message that it couldn't find the correct version of QuickBooks?

Since then, did you re-install QuickBooks?

Is the menu Tools->QuickBooks Billing/Customer Update->Set Preferences still showing the right file and in the right location on your hard drive?