I had exactly the same - I spent two hours on the phone with a techie and he could not explain why the deductions were taking on some employees, not on some, and at different rates on others.
We deleted the payroll items, reinputted, and re-ran the payroll several times. Finally, for no reason, it just started to work correctly and has done since. I would recommend ringing support and screen sharing, and get them to figure it out, but I am not surprised that there is something wrong.
Now, for me, since Week 4, the Pensionsync link has stopped, and I have been told by Intuit today, that it will not send the data to my pension provider because the pay day is not in the pay period. It's taken weeks to get this answer.
The only solution is for me to contact the pension provider and get them to amend their system! I pay Intuit, but not the provider - go figure.
Suffice to say I am leaving QB Online and eventually QB desktop. I have lost hundreds of hours due to their bugs and errors from migration. If I knew what I know now, I would stayed on Desktop and purchased serperate payroll software, and just journalled it in.
A word of warning - be careful with annual leave on migration - that really screwed up, and payroll payments do not deduct the leave balances!