I have had the same issue with a duplicate employee and the whole worked hours not matching on half of my employee's QB reports. After two days on the phone with support, I finally got someone to look at our company file to see what was happening. They opened an investigation into this issue. INV-90255 is the investigation number that might help you when calling in. My problem is still not fixed but tier 3 support will be working with the product developers to hopefully have this resolved by Q3.