It appears that the Job Line Cost Amount is not giving the proper values. The data appeared to loaded successfully. What is included in this group? Does it pull paycheck data, credit card charges, and bills (unpaid and paid)?
Job Costs will match the following QB reports:
Estimate vs Actual - making sure that the following filters are set similarly:
Profit and Loss by Job - but the Account is Job Cost Account is set to yes to filter for only PandL accounts.
We know of no accuracy issues with our current version of QQube at this time.
Since you think the synch is ok, the best thing to do for troubleshooting is to isolate one particular transaction e.g. filter, and look at each line for actual cost.
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