QB Issue Resolution:

Currently, QuickBooks can only support 1099-MISC filing. Since you’ve already checked your company preferences and vendors’ accounts, I recommend reaching out to our support team. They can help you identify the cause why box 6 is being checked on your 1096 form and fix it.

 

Here’s how to contact us:

  1. Go to this link: https://help.quickbooks.intuit.com/en_US/contact.
  2. Choose QuickBooks Desktop.
  3. Select your desktop version.
  4. Choose Running Your Business in QuickBooks and click on Manage Expenses & Vendors.
  5. Click on Get Phone Number.

Resolution for Issue 'Printing Form 1096 on QB Pro 2013 is not checking the correct boxes' available: Yes (Solved).
Source: Intuit Community forum.

Printing Form 1096 on QB Pro 2013 is not checking the correct boxes: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

Support for QB PRO 2013
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Error Recovery for QB PRO 2013 [Canada]
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Additional Support Options: