It is possible that some employees are setup as ‘other names’ in QuickBooks. It is common practice to setup owners and partners as 'other names'.
To import other names:
- Turn on the Setup | QuickBooks | Import 'Other names' from QuickBooks as Employees option.
- Click on Reset next to Employee last sync date in Setup | QuickBooks | Sync History.
- Go to Employee list and click on Sync.