Ran into the same problem. Quickbooks would record the gross amount for each employee on pyroll, as well as the net amount. Resulting in my numbers being astronomically high, and wrong. 

I never used the "Match" feature while categorizing. (Mainly because i didn't quite know what it does tbh). After reading these messages, i decided to do some expirementing. I went back and undid every payroll transaction, and then Matched them. With full trust in the system, it worked. I now have all the gross amounts under "payroll wages", and the taxes under "payroll taxes" 

I hope this helps.