Tax exemption not calculated when a PO Receipt Matched invice is created

HI,
When trying to create a invoice by matching a Receipt to Invoice and could see the correct tax code on the lines which has tax exemption code attached on lines
but when tax is calculated a differnt tax rate code(set as defaulted at tax rules) was calculated automatically by the system.

But when trying to create a standard invoice without po/Receipt matching for the same supplier tax is calculated correctly along with the exemption line.

Any help on this is highly appreciated.

Thanks