@Jeffrey Blattman @Admin @Raymond Lee Highly appreciate any help on this issue.
Are you using Payment Connector? Can you explain exactly how you are performing the PreAuth/PreAuthCapture? Are you performing the PreAuth via REST API? Are you associating line items? Can you submit a private post with your merchant information (and environment, if not sandbox) and details of your PreAuth and PreAuthCapture request so we can take a look (see the "What is the Clover Developer Community" sticky on how to do this)?
The issue here is that the line item of the order you are associating with the PreAuth has a tax rate and (as you noted) the capture API doesn't expose the tax fields necessary for the payment to be adjusted properly. I have created an internal issue to correct this. In the meantime is it possible to use a line item that has no associated taxes? The orders app won't display the taxes correctly but it should no longer display as "PARTIALLY PAID".
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