We've been experiencing a similar issue as well. It's a little different for us though because we use QuickBooks Time, and then import that info into QuickBooks online. What I found is that if I manually make any adjustments to hours (e.g. switch something to a different pay type) when I run payroll the labour cost information will not show up in the projects they have worked on. It is like the timesheet gets 'broken' and the time is now unspecified time. I've had to do a lot of creative overrides and such in QuickBooks Time. And it's now (mostly) working. The odd thing still doesn't report properly, even though payroll ran perfectly.