Hello there, AmericanMotorsports.
To successfully import the data, let's make sure the templates and formats are correct to prevent errors when transferring the file. Though in your case, it looks like the sales tax feature isn't turned on in QuickBooks Desktop. That could be the reason why some transactions are not imported or incorrect.
First, let's turn on the sales tax in QuickBooks Desktop:
Then, manually enter the missing transactions. This way, the Profit and Loss of both software will be the same.
Get back to us if you need more help. We're just around.