One of the first things you'll want to check if you're running into a QuickBooks Desktop integration issue is that you're logged into QuickBooks on an Admin account. A different user with admin rights will not work and may cause unexpected behavior
If payroll items are not being pulled in for your users this could be the cause of a permissions issue. You can update your permissions by selecting Edit --> Integrated Applications --> click Company Preferences tab, click on Buddy Punch and then click on Properties.
You will then want to check the box next to "Allow this application to access Social Security Numbers, customer credit card information, and other personal data" as shown below:
Another main reason a payroll item may not be pulled in is that the Employee in QuickBooks is not assigned a payroll item. You will want to ensure that all Employees have been assigned the correct payroll items.