It's almost certainly to do with tax. It may show $3.61 for shipping but on the invoice it should include $0.29 as additional tax. The difference is 8% which is too coincidental for it not to be due to one setting or another.
I had the check box about sales tax affecting shipping but shouldn't that add sells tax to the shipping not subtract? And that should only affect states where the sales tax is applied? I unchecked the box and see if that has any effect.
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Chris
Reclaimed Components