Using TaxJar automatically computes Taxable Subtotal and submits Other Charges as Shipping, which TaxJar determines to be taxable or untaxable.
To allow concurrent use of TaxJar and classic tax calculations in Big Business, Other Charges marked Taxable are automatically recalculated before submission.
If you are using TaxJar exclusively, you can remove Taxable from all Other Charges and leave this to TaxJar to determine.
The Tax Checkbox on Quote was not updating consitently. This was a regression bug fixed in 13.17.