I am assuming you are using the right company code/tax code combination.
You can try following things:
1. To identify which tax code is being sent to R/3 from Shopping cart, put a break point in SRM FM B46B_TAX_CALCULATE_DOC (version R/3_4.6B and higher) or B31I_TAX_CALCULATE_DOC (version lower to R/3_4.6B).
You can also debug from META_CALCULATE_TAX.
During debugging identify if the tax mapping is done correctly in SRM.
2. You can also try implementing the Badi BBP_TAX_MAP_BADI in SRM for mapping the tax codes etc.
Also refer Note 881086 - Country-specific tax calculation and 999896 - EBP tax codes not correctly mapped to back-end tax codes.
Let me know if this helps.
Regards,
Sushil.
Message was edited by: Sushil Kumar